Merge branch 'master' of https://git.psi.ch/nemu/musrfit

Compilation errors distclean issues

ChangeLog

@@ -2,8 +2,134 @@
 # ChangeLog
 #---------------------------------------------------------------------
 
+changes since 0.18.0
+===================================
+
+changes since 0.17.0
+===================================
+NEW 2016-12-18 for maxLH it is now possible to get the per-run-block maxLH,
+               and the expected maxLH.
+NEW 2016-12-18 musrview allows no to show directly the Fourier transform,
+               and the averaged data/Fourier transform.
+NEW 2016-12-18 added a first full version of an automatic phase correction 
+               for the real part of the Fourier transform. It is based on
+               the algorithm published in JMR 158, 164 (2002).
+NEW 2016-12-18 a couple of improvements in dump_header: (i) it is not
+               only searching in the current directory, but also in all
+               default paths defined in musrfit_startup.xml. (ii) it is
+               now possible also to give only run numbers instead of the
+               full file name.
+NEW 2016-08-24 in musrview it is now possible to enable/disable a
+               crosshair cursor by pressing 'c'.
+NEW 2016-04-28 updated licence info in musredit and added paramList 
+               feature to the msr2data GUI.
+NEW 2016-04-28 msr2data gets a new option: paramList which allows to 
+               extract a subset of all the parameters of a collection
+               of msr-files.
+NEW 2016-04-22 Added the theory function muMinusExpTF for mu minus fits
+NEW 2016-02-23 It is now possible to export the averaged data/Fourier
+CHANGED 2016-12-18 updated the docu.
+CHANGED 2016-12-18 a couple of little improvements in musredit.
+CHANGED 2016-08-10 drop NeXus support for Version < 4.4
+CHANGED 2016-04-26 start-/endTimeBin are now class members. This reduces 
+               the number of recalculations.
+FIXED 2016-08-02 run lists are now properly loaded if containing nS-nE elements.
+
+changes since 0.16.0
+===================================
+NEW 2016-01-22 update of the docu which now describes the RRF option.
+CHANGED 2016-02-17 move the startup XML-files to $HOME/.musrfit
+               rather than having it within $prefix/bin. Increase
+               therefore the version number to 0.17.0
+CHANGED 2016-02-16 if the LEM file is created 2012 or later and the
+               data-file-format tag is still ROOT-NPP or ROOT-PPC, it
+               will automatically switched to MUSR-ROOT. This way red/green
+               issues should be prevented. (see MUSR-314).
+CHANGED 2016-02-16 start migrating the icons of musredit_qt5 to the breeze
+               icons (https://github.com/NitruxSA/breeze-icon-theme).
+               At the same time I start to redesign the musrfit specific
+               icons accordingly (not yet happy with it, but ...).
+
+changes since 0.15.0
+===================================
+NEW 2016-01-22 add RRF fit option. At the same time, the version has been
+               increased to 0.16.0. For details see the documentation.
+FIXED 2015-10-29 TMusrRunHeader didn't map a double vector properly into a
+                 string. The last element was a copy of the 2nd last instead
+		 if the proper last. This is now fixed. Fixed also some
+		 comment typo.
+FIXED 2015-11-11 Fixes the crash of Fourier if the maximal range given in the 
+                 Fourier block is larger than the available.
+CHANGED 2015-11-15 removed unnecessary check form musredit_qt5 msr2data interface.
+
+changes since 0.14.0
+===================================
+NEW 2015-10-26 added a first ported musredit version (Qt4 -> Qt5). At the same
+               the version has been incremented to 0.15.0.
+NEW 2015-09-24 adding a phase optimized real Fourier to musrFT. This is still VERY
+               experimental, and hence only available from within musrFT. Eventually
+               it should make its way into musrview as well. Furthermore the 
+               documentation needs to be written yet. There is only a short not in
+               the command line present.
+NEW 2015-02-23 implemented an average-per-data-set option for musrFT.
+NEW 2015-02-21 add proper Mac icon to musredit
+FIXED 2015-09-22 generating global fit msr-files including a GLOBAL block is working
+                 now as expected.
+FIXED 2015-09-17 in PMsr2Data::PrepareGlobalInputFile() there seem to be 'unmotivated'
+                 break; commands in some loops. They prevent a proper map handling.
+                 Since this is a real puzzle I contacted BMW for clarification. 
+                 2015-09-18: there is only one unmotivated break; cleaned up the code
+                 accordingly.
+FIXED 2015-09-14 any2many export of MusrRoot crashed when first histo group was != 0.
+                 This happend when exporting to PSI-BIN or WKM. This is fixed now.
+FIXED 2015-09-08 fixed error in view_packing for single histo (wrong norm of the theory).
+FIXED 2015-09-04 minor change in Fourier-block output (PMsrHandler::WriteMsrLogFile
+                 and PMsrHandler::WriteMsrLogFile) to avoid truncated range labels.
+FIXED 2015-06-30 changed setf/unsetf bug (PMsr2Data.cpp)
+FIXED 2015-05-15 another path check for HDF5 with ubuntu 15.04
+FIXED 2015-03-16 some minor correction for ASCII export in any2many
+FIXED 2015-02-26 some more bug fixing for average per data set.
+FIXED 2015-02-20 for graphical export in the batch mode, menus mustn't be set.
+CHANGED 2015-08-17 updated ChangeLog which was orphaned since V0.13.0
+CHANGED 2015-08-16 updated the docu
+CHANGED 2015-08-16 added the class PStringNumberList which allow to parse a 
+                   generic encoded list of numbers. Used this class to improve 
+                   PMsrHandler, and improved the runList feature of msr2data. 
+                   For details see the documentation of msr2data.
+CHANGED 2015-06-25 adopted the temperature dependence of the gap function 
+                   (see Eq.(8) of the memo), which breaks the self-consistency. 
+                   Makes it more flexible but requires that the user is using 
+                   his brain.
+CHANGED 2015-06-25 small correction of the skewed Gaussian for extrem parameter 
+                   values.
+CHANGED 2015-05-29 updated docu and removed an unsed variable
+CHANGED 2015-05-29 added a group histo selector in any2many for MusrRoot when 
+                   exporting to a too limited file format as PSI-BIN.
+CHANGED 2015-04-01 update of the technical docu
+CHANGED 2015-02-28 check that FOURIER block phase parameter as parX is not leading 
+                   to an error message.
+CHANGED 2015-02-24 added missing background range from msr-file (musrFT)
+CHANGED 2015-02-24 separated PSI-BIN and PSI-MDU file format
+CHANGED 2015-02-21 make sure that musrFT is found
+CHANGED 2015-02-21 needed to adopted includes for dictionary generation due to 
+                   adding fftw.h in PMusr.h
+CHANGED 2015-02-21 have now README and README.md for automake and bitbucket, 
+                   respectively.
+
 changes since 0.13.0
 ===================================
+NEW 2015-02-23 implemented an average-per-data-set option for musrFT.
+NEW 2015-02-20 add a switch to musrview that it plots initially the Fouier data rather
+               than the time domain data.
+NEW 2015-02-19 added a first preliminary user interface for musrFT within musredit.
+NEW 2015-02-16 changed the data export handling from musrview. It is now more
+               main line and follows the implementation of musrFT.
+NEW 2015-02-13 first implementation of a standalone Fourier transform/plotter: 
+               musrFT. Initially it is meant to be used for HAL-9500, 
+               i.e. Fourier transform WITHOUT lifetime correction.
+               A first simple minded lifetime correction is implemented as well.                
+NEW 2015-02-04 Integration of libBNMR for fitting beta-NMR relaxation data
+	       into automake of musrfit.
 NEW 2014-12-18 first implementation of a GLOBAL block which allows to shorten
                a typical msr-file. Duplicate entries from the RUN blocks can be
                added here. Furthermore, the 'lifetimecorrection' flag is 

README

@@ -1,33 +1,35 @@
-# musrfit - muSR data analysis package #
-
-### Contents ###
-
-This is a data analysis package to analyze time differential muSR data. 
-Currently it allows the following things:
-
-* setting up most commonly used fitting functions for muSR
-* fitting data, including global fits
-* showing the fit results and the residuals
-* showing the Fourier transform of the data
-* extracting easily the fitting parameters to be used in other programs (gnuplot, qtiplot/origin, ...)
-* allows to generate fitting input files for follow-up runs
-* allows to generate global fitting input files based on a single run template
-* allows to implement more sophisticated user functions 
-  (e.g. GL vortex lattice, Meissner screening including low-energy muon stopping profiles)
-
-### Currently supported platforms: ###
-
-* Linux
-* Mac OS X
-* Windows - not really, only for the very brave ones
-
-### Documentation ####
-
-For a more exhaustive user documentation see:
-
-  http://lmu.web.psi.ch/musrfit/user/MUSR/WebHome.html
-
-### Contact ###
-
-<andreas.suter@psi.ch>
-
+README
+
+musrfit - muSR data analysis package
+
+Contents
+--------
+
+This is a data analysis package to analyze time differential muSR and beta-NMR data. 
+Currently it allows the following things:
+
+* setting up most commonly used fitting functions for muSR and beta-NMR
+* fitting data, including global fits
+* showing the fit results and the residuals
+* showing the Fourier transform of the data
+* extracting easily the fitting parameters to be used in other programs (gnuplot, qtiplot/origin, ...)
+* allows to generate fitting input files for follow-up runs
+* allows to generate global fitting input files based on a single run template
+* allows to implement more sophisticated user functions 
+  (e.g. GL vortex lattice, Meissner screening including low-energy muon stopping profiles)
+
+Currently supported platforms:
+
+* Linux
+* Mac OS X
+* Windows - not really, only for the very brave ones
+
+Documentation
+
+For a more exhaustive user documentation see:
+
+  http://lmu.web.psi.ch/musrfit/user/MUSR/WebHome.html
+
+Contact
+
+<andreas.suter@psi.ch>

README.md

@@ -0,0 +1,33 @@
+# musrfit - muSR data analysis package #
+
+### Contents ###
+
+This is a data analysis package to analyze time differential muSR and beta-NMR data. 
+Currently it allows the following things:
+
+* setting up most commonly used fitting functions for muSR and beta-NMR
+* fitting data, including global fits
+* showing the fit results and the residuals
+* showing the Fourier transform of the data
+* extracting easily the fitting parameters to be used in other programs (gnuplot, qtiplot/origin, ...)
+* allows to generate fitting input files for follow-up runs
+* allows to generate global fitting input files based on a single run template
+* allows to implement more sophisticated user functions 
+  (e.g. GL vortex lattice, Meissner screening including low-energy muon stopping profiles)
+
+### Currently supported platforms: ###
+
+* Linux
+* Mac OS X
+* Windows - not really, only for the very brave ones
+
+### Documentation ####
+
+For a more exhaustive user documentation see:
+
+  http://lmu.web.psi.ch/musrfit/user/MUSR/WebHome.html
+
+### Contact ###
+
+<andreas.suter@psi.ch>
+

configure.ac

@@ -1,7 +1,7 @@
 AC_REVISION([m4_esyscmd_s([git describe --always])])
 
 AC_PREREQ(2.63)
-AC_INIT([musrfit],[0.13.0],[andreas.suter@psi.ch])
+AC_INIT([musrfit],[0.18.0],[andreas.suter@psi.ch])
 AC_CONFIG_AUX_DIR(admin)
 AC_CANONICAL_HOST
 #AC_MSG_RESULT([${host} ${host_cpu} ${host_vendor} ${host_os}])
@@ -35,7 +35,7 @@ dnl -----------------------------------------------
 
 #release versioning
 MUSR_MAJOR_VERSION=0
-MUSR_MINOR_VERSION=13
+MUSR_MINOR_VERSION=18
 MUSR_MICRO_VERSION=0
 
 #release versioning
@@ -525,6 +525,9 @@ AC_ARG_ENABLE([NeXus], [AS_HELP_STRING([--enable-NeXus],[build optional NeXus su
          elif test -r /usr/local/hdf5/include/hdf5.h; then
            HDF5_PREFIX="/usr/local/hdf5"
            AC_MSG_RESULT([${HDF5_PREFIX}])
+         elif test -r /usr/include/hdf5/serial/hdf5.h; then
+           HDF5_PREFIX="/usr/include/hdf5/serial"
+           AC_MSG_RESULT([${HDF5_PREFIX}])
          elif test -r /usr/include/hdf5.h; then
            HDF5_PREFIX="/usr"
            AC_MSG_RESULT([${HDF5_PREFIX}])
@@ -551,34 +554,31 @@ AC_ARG_ENABLE([NeXus], [AS_HELP_STRING([--enable-NeXus],[build optional NeXus su
         [AS_HELP_STRING([--with-nexus],[prefix of the NeXus installation, e.g. /usr/local])],
         [NEXUS_PREFIX=$with_nexus
          AC_MSG_CHECKING([whether NeXus can be found at the specified location])
-         if !(test -r ${NEXUS_PREFIX}/include/napi.h); then
+         if !(test -r ${NEXUS_PREFIX}/include/nexus/napi.h); then
            AC_MSG_RESULT([no])
            AC_MSG_ERROR([NeXus cannot be found at the specified path!])
          fi
          AC_MSG_RESULT([${NEXUS_PREFIX}])],
-        [PKG_CHECK_MODULES(NEXUS, nexus >= 4.1, [NEXUS_FOUND=1],
+        [PKG_CHECK_MODULES(NEXUS, nexus >= 4.4, [NEXUS_FOUND=1],
          [AC_MSG_CHECKING([whether NeXus is installed in a standard location])
-          if test -r /usr/local/include/napi.h; then
-            NEXUS_PREFIX="/usr/local"
-            AC_MSG_RESULT([${NEXUS_PREFIX}])
-         elif test -r /usr/local/nexus/include/napi.h; then
-           NEXUS_PREFIX="/usr/local/nexus"
+          if test -r /usr/local/include/nexus/napi.h; then
+           NEXUS_PREFIX="/usr/local"
            AC_MSG_RESULT([${NEXUS_PREFIX}])
-         elif test -r /usr/include/napi.h; then
-           NEXUS_PREFIX="/usr"
-           AC_MSG_RESULT([${NEXUS_PREFIX}])
-         elif test -r /sw/include/napi.h; then
+          elif test -r /sw/include/nexus/napi.h; then
            NEXUS_PREFIX="/sw"
            AC_MSG_RESULT([${NEXUS_PREFIX}])
-         elif test -r /opt/local/include/napi.h; then
+          elif test -r /opt/local/include/nexus/napi.h; then
            NEXUS_PREFIX="/opt/local"
            AC_MSG_RESULT([${NEXUS_PREFIX}])
-         else
+          elif test -r /opt/nexus/include/nexus/napi.h; then
+           NEXUS_PREFIX="/opt/nexus"
+           AC_MSG_RESULT([${NEXUS_PREFIX}])
+          else
            AC_MSG_RESULT([no])
            AC_MSG_ERROR(
-           [NeXus not found. Please call configure with the --with-nexus option.
+           [NeXus Version >= 4.4 not found. Please call configure with the --with-nexus option.
            This tells configure where to find the NeXus headers,
-           e.g. --with-nexus=/usr/local/nexus]
+           e.g. --with-nexus=/opt/nexus]
            )
          fi
         ]
@@ -586,8 +586,27 @@ AC_ARG_ENABLE([NeXus], [AS_HELP_STRING([--enable-NeXus],[build optional NeXus su
     )
     AC_SUBST(NEXUS_PREFIX)
     if test "${NEXUS_FOUND}" != "1"; then
-      NEXUS_LIBS="-L${NEXUS_PREFIX}/lib -lNeXus"
-      NEXUS_CFLAGS="-I${NEXUS_PREFIX}/include"
+      dnl get suffix for the NeXus library depending on the OS
+      AC_REQUIRE([AC_CANONICAL_HOST])
+      AS_CASE([$host_os],
+       [linux*], [NEXUS_SUFFIX="so"],
+       [darwin*], [NEXUS_SUFFIX="dylib"],
+       [*cygwin*], [NEXUS_SUFFIX="dll"],
+       [AC_MSG_ERROR([NeXus check: Your platform is not currently supported])]
+      )
+      AC_MSG_NOTICE([NeXus Suffix Result: "${NEXUS_SUFFIX}"])
+      if test -r ${NEXUS_PREFIX}/lib/libNeXus.${NEXUS_SUFFIX}; then
+        NEXUS_LIB_DIR="lib"
+      elif test -r ${NEXUS_PREFIX}/lib64/libNeXus.${NEXUS_SUFFIX}; then
+        NEXUS_LIB_DIR="lib64"
+      else
+        AC_MSG_ERROR(
+         [Couldn't find the NeXus library.]
+        )
+      fi
+
+      NEXUS_LIBS="-L${NEXUS_PREFIX}/${NEXUS_LIB_DIR} -lNeXus"
+      NEXUS_CFLAGS="-I${NEXUS_PREFIX}/include/nexus"
     fi
     AC_SUBST(NEXUS_LIBS)
     AC_SUBST(NEXUS_CFLAGS)
@@ -733,6 +752,12 @@ dnl -----------------------------------------------
 
 AC_ARG_ENABLE([ASlibs], [AS_HELP_STRING([--enable-ASlibs],[build optional AS plug-ins [default=no]])],[BUILD_AS_LIBS=1], [BUILD_AS_LIBS=0])
 
+dnl -----------------------------------------------
+dnl Ask user if BNMRlibs should be built
+dnl -----------------------------------------------
+
+AC_ARG_ENABLE([BNMRlibs], [AS_HELP_STRING([--enable-BNMRlibs],[build optional BNMR plug-ins [default=no]])],[BUILD_BNMR_LIBS=1], [BUILD_BNMR_LIBS=0])
+
 dnl -----------------------------------------------
 dnl Set some paths and flags for PMusr, MusrRoot, TLemRunHeader, Class_MuSR_PSI, mud, NeXus (if enabled), etc.
 dnl -----------------------------------------------
@@ -780,6 +805,14 @@ if test "${PNEXUS_ENABLED}" = "1"; then
   AC_SUBST(PNEXUS_CXXFLAGS)
 fi
 
+if test "${BUILD_BNMR_LIBS}" = "1"; then
+  BNMRLIBS_SRCDIR="${SRCDIR}/external/libBNMR"
+  BNMRLIBS_LIBS="${BNMRLIBS_SRCDIR}/libBNMR.la"
+  BNMRLIBS_CFLAGS="-I${BNMRLIBS_SRCDIR}"
+  AC_SUBST(BNMRLIBS_LIBS)
+  AC_SUBST(BNMRLIBS_CFLAGS)
+fi
+
 if test "${BUILD_BMW_LIBS}" = "1"; then
   BMWTOOLS_SRCDIR="${SRCDIR}/external/BMWtools"
   BMWTOOLS_LIBS="${BMWTOOLS_SRCDIR}/libBMWtools.la"
@@ -841,6 +874,8 @@ if test "x$enable_editor" != "xno"; then
 
   echo "Additional checks for musredit/musrgui ..."
 
+  QT5MINVER=5.4
+
   case "$host" in
     *-*-cygwin)
       QT4MINVER=4.5
@@ -853,6 +888,7 @@ if test "x$enable_editor" != "xno"; then
   QT3_FOUND=no
   QT3MT_FOUND=no
   QT4_FOUND=no
+  QT5_FOUND=no
   QMAKEBIN=""
   QTEDITOR=none
 
@@ -926,14 +962,58 @@ if test "x$enable_editor" != "xno"; then
         fi]
   )
 
+  AC_ARG_WITH([qt5],
+        [AS_HELP_STRING([--with-qt5],[prefix of the Qt5 installation, e.g. /usr/lib64/qt5/])],
+        [QT5_PREFIX=$with_qt5
+        AC_MSG_CHECKING([whether qmake for Qt5 can be found at the specified location])
+        for QMAKE in qmake qmake-qt5
+        do
+          if test -x "${QT5_PREFIX}/bin/${QMAKE}"; then
+            QMAKEVERSIONSTRING="$(${QT5_PREFIX}/bin/${QMAKE} -v 2>&1)"
+            for a in $QMAKEVERSIONSTRING
+            do
+              if test "$(expr "$a" : '\(..\)')" = "5."; then
+                QMAKEBIN="${QT5_PREFIX}/bin/${QMAKE}"
+                QTEDITOR=musredit_qt5
+                AC_MSG_RESULT([${QMAKEBIN}])
+                break
+              fi
+            done
+            if test "x${QMAKEBIN}" != "x"; then
+              break
+            fi
+          fi
+        done
+
+        if test "x${QMAKEBIN}" = "x"; then
+          AC_MSG_RESULT([no])
+          AC_MSG_ERROR([qmake for Qt5 cannot be found in ${QT5_PREFIX}/bin!])
+        fi
+
+        if test "x${QT4PRESENT}" = "xyes"; then
+          AC_MSG_WARN([Qt4 and Qt5 directories have been given -- only the Qt5 information will be used and only musredit will be built!])
+        fi],
+        [if test "x${QMAKEBIN}" = "x"; then
+          PKG_CHECK_MODULES(QT5, Qt5WebKit >= $QT5MINVER Qt5Xml >= $QT5MINVER, [QT5_FOUND=yes],
+            [AC_MSG_NOTICE([Qt5 (including Qt5WebKit and Qt5Xml) not found!])
+             PKG_CHECK_MODULES(QT3, qt >= 3.3.0 qt < 4.0, [QT3_FOUND=yes],
+              [PKG_CHECK_MODULES(QT3MT, qt-mt >= 3.3.0 qt-mt < 4.0, [QT3MT_FOUND=yes], [QT3MT_FOUND=no])]
+            )]
+          )
+        fi]
+  )
+
   if test "x${QMAKEBIN}" = "x"; then
-    if test "x${QT3_FOUND}" = "xno" && test "x${QT3MT_FOUND}" = "xno" && test "x${QT4_FOUND}" = "xno"; then
-      AC_MSG_WARN([No suitable version of either Qt4 or Qt3 has been found! musredit/musrgui will not be built in this stage!])
+    if test "x${QT3_FOUND}" = "xno" && test "x${QT3MT_FOUND}" = "xno" && test "x${QT4_FOUND}" = "xno" && test "x${Qt5_FOUND}" = "xno"; then
+      AC_MSG_WARN([No suitable version of either Qt5, Qt4 or Qt3 has been found! musredit/musrgui will not be built in this stage!])
     else
       # Check for qmake on the basis of the pkg-config information
       QTPATH=none
 
-      if test "x$QT4_FOUND" = "xyes"; then
+      if test "x$QT5_FOUND" = "xyes"; then
+        QTPATH=$(pkg-config --variable=prefix Qt5WebKit)
+        QTEDITOR=musredit_qt5
+      elif test "x$QT4_FOUND" = "xyes"; then
         QTPATH=$(pkg-config --variable=prefix QtWebKit)
         QTEDITOR=musredit
       elif test "x$QT3_FOUND" = "xyes"; then
@@ -946,7 +1026,29 @@ if test "x$enable_editor" != "xno"; then
 
       AC_MSG_CHECKING([for qmake])
       if test "x${QTPATH}" != "xnone"; then
-        if test "x$QTEDITOR" = "xmusredit"; then
+        if test "x$QTEDITOR" = "xmusredit_qt5"; then
+          for QMAKE in qmake-qt5 qmake-qt54 qmake-qt55
+          do
+            if test -x "${QTPATH}/bin/${QMAKE}"; then
+              QMAKEBIN="${QTPATH}/bin/${QMAKE}"
+              AC_MSG_RESULT([${QMAKEBIN}])
+              break
+            fi
+          done
+          if test "x${QMAKEBIN}" = "x"; then
+            if test -x "${QTPATH}/bin/qmake"; then
+              QMAKEVERSIONSTRING="$(${QTPATH}/bin/qmake -v 2>&1)"
+              for a in $QMAKEVERSIONSTRING
+              do
+                if test "$(expr "$a" : '\(..\)')" = "5."; then
+                  QMAKEBIN="${QTPATH}/bin/qmake"
+                  AC_MSG_RESULT([${QMAKEBIN}])
+                  break
+                fi
+              done
+            fi
+          fi
+        elif test "x$QTEDITOR" = "xmusredit"; then
           for QMAKE in qmake-qt4 qmake-qt46 qmake-qt47 qmake-qt48
           do
             if test -x "${QTPATH}/bin/${QMAKE}"; then
@@ -993,13 +1095,14 @@ if test "x$enable_editor" != "xno"; then
         fi
         if test "x${QMAKEBIN}" = "x"; then
           AC_MSG_RESULT([no])
-          AC_MSG_WARN([If Qt4 or Qt3 are present but have not been detected, try using the --with-qt4 or --with-qt3 options!])
+          AC_MSG_WARN([If Qt5, Qt4 or Qt3 are present but have not been detected, try using the --with-qt5, --with-qt4 or --with-qt3 options!])
         fi
       fi
     fi
   fi
 fi
 
+AM_CONDITIONAL([BUILD_MUSREDIT_QT5], [test "x$enable_editor" != "xno" && test "x${QMAKEBIN}" != "x" && test "x${QTEDITOR}" = "xmusredit_qt5"])
 AM_CONDITIONAL([BUILD_MUSREDIT], [test "x$enable_editor" != "xno" && test "x${QMAKEBIN}" != "x" && test "x${QTEDITOR}" = "xmusredit"])
 AM_CONDITIONAL([BUILD_MUSRGUI], [test "x$enable_editor" != "xno" && test "x${QMAKEBIN}" != "x" && test "x${QTEDITOR}" = "xmusrgui"])
 
@@ -1111,6 +1214,7 @@ AM_CONDITIONAL([PNEXUS_ENABLED], [test "${PNEXUS_ENABLED}" = "1"])
 AM_CONDITIONAL([BUILD_CUBALIB], [test "${BUILD_CUBA}" = "1"])
 AM_CONDITIONAL([BUILD_BMWLIBS], [test "${BUILD_BMW_LIBS}" = "1"])
 AM_CONDITIONAL([BUILD_ASLIBS], [test "${BUILD_AS_LIBS}" = "1"])
+AM_CONDITIONAL([BUILD_BNMRLIBS], [test "${BUILD_BNMR_LIBS}" = "1"])
 
 AC_CONFIG_FILES([Makefile \
                  src/Makefile \
@@ -1151,6 +1255,12 @@ AC_CONFIG_FILES([Makefile \
 		 src/external/libSpinValve/classes/Makefile \
                  src/external/libPhotoMeissner/Makefile \
                  src/external/libPhotoMeissner/classes/Makefile \
+                 src/external/libGbGLF/Makefile \
+                 src/external/libBNMR/Makefile \
+                 src/musredit_qt5/Makefile \
+                 src/musredit/Makefile \
+                 src/musrgui/Makefile \
+                 src/musredit_qt5/musredit_startup.xml \
                  src/musredit/musredit_startup.xml \
                  src/musrgui/musrgui_startup.xml])
 
@@ -1160,10 +1270,16 @@ if test "x$enable_editor" != "xno" && test "x$QMAKEBIN" != "x"; then
 
   echo "Configuring ${QTEDITOR} ..."
 
+  if test "x${QTEDITOR}" = "xmusredit_qt5"; then
+    QTEDITOR_PRO="musredit"
+  else
+    QTEDITOR_PRO=${QTEDITOR}
+  fi
+
   echo "Changing directory to src/${QTEDITOR} and calling"
-  echo "${QMAKEBIN} CC=${CC} CXX=${CXX} PREFIX=${INSTALLDIR} ${QTEDITOR}.pro"
+  echo "${QMAKEBIN} CC=${CC} CXX=${CXX} PREFIX=${INSTALLDIR} ${QTEDITOR_PRO}.pro"
   cd src/${QTEDITOR}
-  ${QMAKEBIN} CC=${CC} CXX=${CXX} PREFIX=${INSTALLDIR} ${QTEDITOR}.pro
+  ${QMAKEBIN} CC=${CC} CXX=${CXX} PREFIX=${INSTALLDIR} ${QTEDITOR_PRO}.pro
   cd ../..
 
 fi
@@ -1270,6 +1386,11 @@ if test "${BUILD_AS_LIBS}" -eq 1; then
 else
   echo "     ASlibs:                              no"
 fi
+if test "${BUILD_BNMR_LIBS}" -eq 1; then
+  echo "     BNMRlibs:                            yes"
+else
+  echo "     BNMRlibs:                            no"
+fi
 if test "${BUILD_BMW_LIBS}" -eq 1; then
   echo "     BMWlibs:                             yes"
 else
@@ -1277,21 +1398,27 @@ else
 fi
 echo ""
 echo "   Qt musrfit editors:"
+if test "x$enable_editor" != "xno" && test "x${QMAKEBIN}" != "x" && test "x${QTEDITOR}" = "xmusredit_qt5"; then
+  echo "     musredit (Qt5):                      yes"
+else
+  echo "     musredit (Qt5):                      no"
+fi
 if test "x$enable_editor" != "xno" && test "x${QMAKEBIN}" != "x" && test "x${QTEDITOR}" = "xmusredit"; then
   echo "     musredit (Qt4):                      yes"
 else
   echo "     musredit (Qt4):                      no"
 fi
 if test "x$enable_editor" != "xno" && test "x${QMAKEBIN}" != "x" && test "x${QTEDITOR}" = "xmusrgui"; then
-  echo "     musrgui (Qt3):                       yes"
+  echo "     musrgui  (Qt3):                      yes"
 else
-  echo "     musrgui (Qt3):                       no"
+  echo "     musrgui  (Qt3):                      no"
 fi
 echo ""
 echo ""
 echo "   Installation directories:"
 echo "   -------------------------"
 echo ""
-echo "   Programs and XML configuration files:  ${INSTALLDIR}/bin"
-echo "   Documentation:                         ${DOCDIR}"
+echo "   Programs:                ${INSTALLDIR}/bin"
+echo "   XML configuration files: ${HOME}/.musrfit"  
+echo "   Documentation:           ${DOCDIR}"
 echo ""

doc/examples/BMWlibs/data/libGapIntegrals-test.dat

@@ -12,15 +12,25 @@ ENERGY: 4200
 # here the data will follow
 data
 # x, y, error y
-0.02, 12.0, 0.5
-0.1, 11.8, 0.8
-0.2, 9.9, 0.4
-0.33, 7.2, 0.15
-0.41, 3.8, 0.38
-0.5, 2.7, 0.5
-0.64, 1.0, 0.7
-0.7, 0.1, 0.2
-0.8, 0.0, 0.8
-0.9, 0.1, 0.5
-1.2, 0.0, 0.1
-
+0.0318411, 7.77455, 0.2
+0.0629929, 7.9869, 0.15
+0.113914, 7.64209, 0.15
+0.202492, 7.37699, 0.15
+0.302725, 7.70893, 0.12
+0.447456, 7.77565, 0.12
+0.611685, 7.45768, 0.12
+0.813613, 7.19287, 0.12
+1.00822, 7.57813, 0.12
+1.24793, 7.31343, 0.12
+1.50635, 7.16818, 0.12
+1.74591, 6.99634, 0.12
+1.99795, 6.90414, 0.12
+2.25061, 6.41393, 0.12
+2.4958, 6.66666, 0.12
+2.75514, 5.93766, 0.12
+3.00753, 5.61992, 0.12
+3.26056, 4.89091, 0.12
+3.49414, 4.52005, 0.08
+3.75356, 3.73799, 0.08
+3.99425, 2.84974, 0.08
+4.30518, 1.35139, 0.08

doc/examples/BMWlibs/test-libGapIntegrals-ASCII.msr

@@ -2,18 +2,16 @@ Test superconductor data
 ###############################################################
 FITPARAMETER
 #      Nr. Name        Value     Step      Pos_Error  Boundaries
-        1 lambdaInvSq0 11.69     0.39        none        
-        2 Tc          0.558     0.018       none        0       2       
-        3 Delta0      0.0673    0.0035      none        
-        4 aG          1         0           none        
+        1 lambdaInvSq0 7.983     -0.042      0.042       
+        2 Tc          4.470     -0.015      0.016       0       5       
+        3 Delta0      1.547     -0.026      0.027       
+        4 c0          1.468     0           none        
+        5 aG          1.33333   0           none        
 
 ###############################################################
 THEORY
 asymmetry      1
-userFcn  libGapIntegrals TGapSWave 2 3 4
-
-###############################################################
-#FUNCTIONS
+userFcn  libGapIntegrals TGapDWave 2 3 4 5
 
 ###############################################################
 RUN data/libGapIntegrals-test PIM3 PSI ASCII   (name beamline institute data-file-format)
@@ -26,15 +24,15 @@ packing         1
 ###############################################################
 COMMANDS
 MINIMIZE
-HESSE
-#MINOS
+#HESSE
+MINOS
 SAVE
 
 ###############################################################
 PLOT 8   (non muSR plot)
 runs     1   
-range    0   1.5
+range    0   6
 
 ###############################################################
-STATISTIC --- 2014-10-28 10:40:31
-  chisq = 14.3, NDF = 8, chisq/NDF = 1.790471
+STATISTIC --- 2015-06-25 08:39:03
+  chisq = 58.3, NDF = 19, chisq/NDF = 3.066272

doc/examples/UserFcn/Makefile.PUserFcn

@@ -0,0 +1,60 @@
+#---------------------------------------------------
+# get compilation flags from root-config
+
+ROOTCFLAGS    = $(shell $(ROOTSYS)/bin/root-config --cflags)
+
+#---------------------------------------------------
+
+OS            = LINUX
+CXX           = g++
+CXXFLAGS      = -O3 -Wall -Wno-trigraphs -fPIC
+LOCALINCLUDE  = .
+ROOTINCLUDE   = $(ROOTSYS)/include
+INCLUDES      = -I$(LOCALINCLUDE) -I$(ROOTINCLUDE)
+LD            = g++
+LDFLAGS       =
+SOFLAGS       = -O -shared
+
+# the output from the root-config script:
+CXXFLAGS      += $(ROOTCFLAGS)
+LDFLAGS       +=
+
+# some definitions: headers (used to generate *Dict* stuff), sources, objects,...
+OBJS =
+OBJS += PUserFcn.o PUserFcnDict.o
+
+SHLIB = libPUserFcn.so
+
+# make the shared lib:
+#
+all:  $(SHLIB)
+
+$(SHLIB): $(OBJS)
+	@echo "---> Building shared library $(SHLIB) ..."
+	/bin/rm -f $(SHLIB)
+	$(LD) $(OBJS) $(SOFLAGS) -o $(SHLIB)
+	@echo "done"
+
+# clean up: remove all object file (and core files)
+# semicolon needed to tell make there is no source
+# for this target!
+#
+clean:; 	@rm -f $(OBJS) *Dict* core*
+	@echo "---> removing $(OBJS)"
+
+#
+$(OBJS): %.o: %.cpp
+	$(CXX) $(INCLUDES) $(CXXFLAGS) -c $<
+
+# Generate the ROOT CINT dictionary
+
+PUserFcnDict.cpp: PUserFcn.h PUserFcnLinkDef.h
+	@echo "Generating dictionary $@..."
+	rootcint -f $@ -c -p -I$(ROOTINCLUDE) $^
+
+install: all
+	@echo "Installing shared lib: libTApproximation.so"
+ifeq ($(OS),LINUX)
+	cp -pv $(SHLIB) $(ROOTSYS)/lib
+	cp -pv $(LOCALINCLUDE)/*.h $(ROOTSYS)/include
+endif

doc/examples/UserFcn/PUserFcn.cpp

@@ -0,0 +1,59 @@
+/***************************************************************************
+
+  PUserFcn.cpp
+
+  Author: Andreas Suter
+  e-mail: andreas.suter@psi.ch
+
+***************************************************************************/
+
+/***************************************************************************
+ *   Copyright (C) 2007-2016 by Andreas Suter                              *
+ *   andreas.suter@psi.ch                                                  *
+ *                                                                         *
+ *   This program is free software; you can redistribute it and/or modify  *
+ *   it under the terms of the GNU General Public License as published by  *
+ *   the Free Software Foundation; either version 2 of the License, or     *
+ *   (at your option) any later version.                                   *
+ *                                                                         *
+ *   This program is distributed in the hope that it will be useful,       *
+ *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
+ *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
+ *   GNU General Public License for more details.                          *
+ *                                                                         *
+ *   You should have received a copy of the GNU General Public License     *
+ *   along with this program; if not, write to the                         *
+ *   Free Software Foundation, Inc.,                                       *
+ *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
+ ***************************************************************************/
+
+#include <iostream>
+using namespace std;
+
+#include <cassert>
+
+#include "PUserFcn.h"
+
+ClassImp(PUserFcn)
+
+//------------------------------------------------------
+/**
+ * <p> user function example: polynome of 3rd order
+ *
+ * \f[ = \sum_{k=0}^3 c_k t^k \f]
+ *
+ * <b>meaning of paramValues:</b> \f$c_0\f$, \f$c_1\f$, \f$c_2\f$, \f$c_3\f$
+ *
+ * <b>return:</b> function value
+ *
+ * \param t time in \f$(\mu\mathrm{s})\f$, or x-axis value for non-muSR fit
+ * \param param parameter vector
+ */
+Double_t PUserFcn::operator()(Double_t t, const std::vector<Double_t> &param) const
+{
+  // expected parameters: c0, c1, c2, c3
+
+  assert(param.size() == 4);
+
+  return param[0] + param[1]*t + param[2]*t*t + param[3]*t*t*t;
+}

doc/examples/UserFcn/PUserFcn.h

@@ -0,0 +1,58 @@
+/***************************************************************************
+
+  PUserFcn.h
+
+  Author: Andreas Suter
+  e-mail: andreas.suter@psi.ch
+
+***************************************************************************/
+
+/***************************************************************************
+ *   Copyright (C) 2007-2016 by Andreas Suter                              *
+ *   andreas.suter@psi.ch                                                  *
+ *                                                                         *
+ *   This program is free software; you can redistribute it and/or modify  *
+ *   it under the terms of the GNU General Public License as published by  *
+ *   the Free Software Foundation; either version 2 of the License, or     *
+ *   (at your option) any later version.                                   *
+ *                                                                         *
+ *   This program is distributed in the hope that it will be useful,       *
+ *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
+ *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
+ *   GNU General Public License for more details.                          *
+ *                                                                         *
+ *   You should have received a copy of the GNU General Public License     *
+ *   along with this program; if not, write to the                         *
+ *   Free Software Foundation, Inc.,                                       *
+ *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
+ ***************************************************************************/
+
+#ifndef _PUSERFCN_H_
+#define _PUSERFCN_H_
+
+#include <vector>
+
+#include "PUserFcnBase.h"
+
+/**
+ * <p>User function example class. Polynome of 3rd order.
+ */
+class PUserFcn : public PUserFcnBase
+{
+  public:
+    PUserFcn() {}
+    ~PUserFcn() {}
+
+    // global user-function-access functions, here without any functionality
+    Bool_t NeedGlobalPart() const { return false; }
+    void SetGlobalPart(vector<void*> &globalPart, UInt_t idx) { }
+    Bool_t GlobalPartIsValid() const { return true; }
+
+    // function operator
+    Double_t operator()(Double_t t, const std::vector<Double_t> &param) const;
+
+  // definition of the class for the ROOT dictionary
+  ClassDef(PUserFcn, 1)
+};
+
+#endif // _PUSERFCN_H_

doc/examples/UserFcn/PUserFcnLinkDef.h

@@ -0,0 +1,15 @@
+/***************************************************************************
+
+  PUserFcnLinkDef.h
+
+***************************************************************************/
+
+#ifdef __CINT__
+
+#pragma link off all globals;
+#pragma link off all classes;
+#pragma link off all functions;
+
+#pragma link C++ class PUserFcn+;
+
+#endif //__CINT__

doc/examples/UserFcn/README

@@ -0,0 +1,89 @@
+/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
+
+Simple Example for a User Function without Global Part
+
+/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
+
+Goal: define a user function which implements a polynom
+      of 3rd order.
+
+For details see: http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFit.html#A_6_User_Functions
+
+Implementation:
+      3 Files are needed:
+
+      1) A header file which defines your user function
+         interface.
+ 
+         In the example here it is called PUserFcn.h
+
+         Please rename it in your case to something more
+         sensible, e.g. PMyPoly.h. At the same time also 
+         rename correspondingly the class name in your 
+         header file, i.e. PUserFcn -> PMyPoly. This will
+         be at 4 places in the header file of this example.
+
+      2) The source file which defines your user function.
+
+         In the example here it is called PUserFcn.cpp
+
+         Please rename it accordingly to the header file.
+         In case the header file is called PMyPoly.h, the
+         source file will need to be called PMyPoly.cpp.
+         As for the header file, the class names need to 
+         be adopted: PUserFcn -> PMyPoly.
+
+         In the source file change the operator implementation
+         (Double_t PUserFcn::operator()(Double_t t, 
+                   const std::vector<Double_t> &param) const)
+         to whatever you need.
+
+      3) There is another header file needed to generate
+         the necessary ROOT dictionary.
+
+         In this example it is called PUserFcnLinkDef.h
+
+         Here you only will need to find PUserFcn+ and 
+         replace it with your class name, e.g. PMyPoly+
+
+Generate Code:
+      You will find the Makefil.PUserFcn which generates
+      the needed shared library for your user function.
+
+      Again, if your user function is called PMyPoly, you
+      will need to replace things accordingly in the 
+      Makefile, i.e.
+
+      Makefile.PUserFcn -> Makefile.PMyPoly
+
+      In the Makefile:
+
+      PUserFcn.o      ->  PMyPoly.o
+      PUserFcnDict.o  ->  PMyPolyDict.o
+      libPUserFcn.so  ->  libPMyPoly.so
+
+      To create the shared library do:
+
+      make -f Makefile.PUserFcn
+
+      on the command line. This should create a file      
+      libPUserFcn.so.
+
+      Next call on the command line:
+
+      make -f Makefile.PUserFcn install
+
+      This will copy the shared library to the correct
+      place. 
+
+      You also will need to make sure that the system is
+      finding the shared library, either by setting
+      LD_LIBRARY_PATH or by calling /sbin/ldconfig as 
+      superuser/root assuming you are using linux.
+
+Example msr-file:
+      You will find an example msr-file test-asy-MUS.msr
+      which is using PUserFcn. The example is UN-PHYSICALLY
+      it is just to show how to use a user function. 
+      
+ 

doc/examples/UserFcn/test-asy-MUD.msr

@@ -0,0 +1,55 @@
+MgB12H12 No2 ZF T=150
+###############################################################
+FITPARAMETER
+#      Nr. Name        Value     Step      Pos_Error  Boundaries
+        1 alpha       1         0           none        0       2       
+        2 asy         0.1650    0.0027      none        0       0.33    
+        3 c0          1.047     0.016       none        
+        4 c1          -0.1957   0.0038      none        
+        5 c2          0.0216    0.0011      none        
+        6 c3          -0.00119  0.00011     none        
+
+###############################################################
+THEORY
+asymmetry      2
+userFcn  libPUserFcn PUserFcn 3 4 5 6
+
+###############################################################
+RUN data/000100 XXXX TRIUMF MUD   (name beamline institute data-file-format)
+fittype         2         (asymmetry fit)
+alpha           1
+map             0    0    0    0    0    0    0    0    0    0    0
+forward         1 
+backward        2 
+background      79      391     80      409        # estimated bkg: 21.0833 / 17.2249
+data            438     12785   436     12787   
+t0              432.0   431.0   
+fit             0       8      
+packing         100
+
+###############################################################
+COMMANDS
+MINIMIZE
+MINOS
+#HESSE
+SAVE
+
+###############################################################
+FOURIER
+units            Gauss   # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
+fourier_power    12
+apodization      NONE    # NONE, WEAK, MEDIUM, STRONG
+plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
+phase            8
+#range_for_phase_correction 50.0 70.0
+range            0    2000
+dc-corrected     true
+
+###############################################################
+PLOT 2   (asymmetry plot)
+runs     1   
+range    0   9   0   0.22
+
+###############################################################
+STATISTIC --- 2016-06-22 09:34:01
+  chisq = 152.4, NDF = 97, chisq/NDF = 1.571461

doc/examples/test-asy-HAL9500-RRF.msr

@@ -0,0 +1,178 @@
+MnSi, FLC68.2, 50 K                                           
+###############################################################
+FITPARAMETER
+#      Nr. Name       Value     Step      Pos_Error Boundaries   
+        1 rate_1      1.680     0.019       none        
+        2 field_1     1589.71   0.20        none        
+        3 rate_2      1.863     0.065       none        
+        4 field_2     788.86    0.49        none        
+
+        5 alpha_f15   1.0029    0.0015      none        
+        6 frac_f15    0.7350    0.0090      none        
+        7 asym_f15    0.2713    0.0043      none        0       none    
+        8 phase_f15   79.37     0.80        none        
+
+        9 alpha_f26   0.9996    0.0015      none        
+       10 frac_f26    0.7408    0.0085      none        
+       11 asym_f26    0.3029    0.0046      none        0       none    
+       12 phase_f26   30.22     0.73        none        
+
+       13 alpha_f37   1.0003    0.0015      none        
+       14 frac_f37    0.88      0.23        none        
+       15 asym_f37    0.0126    0.0045      none        0       none    
+       16 phase_f37   58.0      15.0        none        
+
+       17 alpha_f48   0.9999    0.0015      none        
+       18 frac_f48    0.7344    0.0084      none        
+       19 asym_f48    0.2929    0.0043      none        0       none    
+       20 phase_f48   -33.13    0.76        none        
+
+       21 alpha_b15   0.9991    0.0013      none        
+       22 frac_b15    0.7439    0.0077      none        
+       23 asym_b15    0.2807    0.0038      none        0       none    
+       24 phase_b15   164.98    0.68        none        
+
+       25 alpha_b26   1.0003    0.0013      none        
+       26 frac_b26    0.7331    0.0078      none        
+       27 asym_b26    0.2810    0.0038      none        0       none    
+       28 phase_b26   119.49    0.70        none        
+
+       29 alpha_b37   0.9989    0.0012      none        
+       30 frac_b37    0.7504    0.0078      none        
+       31 asym_b37    0.2755    0.0037      none        0       none    
+       32 phase_b37   102.07    0.69        none        
+
+       33 alpha_b48   0.9990    0.0012      none        
+       34 frac_b48    0.7391    0.0080      none        
+       35 asym_b48    0.2763    0.0039      none        0       none    
+       36 phase_b48   37.66     0.67        none        
+
+###############################################################
+THEORY
+asymmetry   fun1
+simplExpo      1          (rate)
+TFieldCos   map3  fun3       (phase frequency)
++
+asymmetry   fun2
+simplExpo      3          (rate)
+TFieldCos   map3  fun4       (phase frequency)
+
+###############################################################
+FUNCTIONS
+fun1 = map1 * map2
+fun2 = (1 - map1) * map2
+fun3 = gamma_mu * par2
+fun4 = gamma_mu * par4
+
+###############################################################
+GLOBAL
+fittype         3         (asymmetry RRF fit)
+fit             0.0005  6      
+rrf_freq        7.15     T
+rrf_packing     300     
+rrf_phase       0.00    
+
+###############################################################
+# Fw1-Fw5 +++++++
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+alpha           5
+map             6    7    8    0    0    0    0    0    0    0    0
+forward         2 
+backward        6 
+background      500     15000   500     15000      # estimated bkg: 0.0492 / 0.0501
+data            20158   409500  20130   409500  
+t0              20108.0 20080.0 
+
+# Fw2-Fw6 +++++++
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+alpha           9
+map            10   11   12    0    0    0    0    0    0    0    0
+forward         3 
+backward        7 
+background      500     15000   500     15000      # estimated bkg: 0.0501 / 0.0451
+data            20138   409500  20121   409500  
+t0              20088.0 20071.0 
+
+# Fw3-Fw7 +++++++
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+alpha           13
+map            14   15   16    0    0    0    0    0    0    0    0
+forward         3 
+backward        8 
+background      500     15000   500     15000      # estimated bkg: 0.0501 / 0.0449
+data            20111   409500  20116   409500  
+t0              20061.0 20066.0 
+
+# Fw4-Fw8 +++++++
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+alpha           17
+map            18   19   20    0    0    0    0    0    0    0    0
+forward         5 
+backward        9 
+background      500     15000   500     15000      # estimated bkg: 0.0560 / 0.0462
+data            20121   409500  20082   409500  
+t0              20071.0 20032.0 
+
+# Bw1-Bw5 +++++++
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+alpha           21
+map            22   23   24    0    0    0    0    0    0    0    0
+forward         10 
+backward        14 
+background      500     15000   500     15000      # estimated bkg: 0.0641 / 0.0806
+data            20072   409500  20067   409500  
+t0              20022.0 20017.0 
+
+# Bw2-Bw6 +++++++
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+alpha           25
+map            26   27   28    0    0    0    0    0    0    0    0
+forward         11 
+backward        15 
+background      500     15000   500     15000      # estimated bkg: 0.0689 / 0.0768
+data            20076   409500  20069   409500  
+t0              20026.0 20019.0 
+
+# Bw3-Bw7 +++++++
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+alpha           29
+map            30   31   32    0    0    0    0    0    0    0    0
+forward         12 
+backward        16 
+background      500     15000   500     15000      # estimated bkg: 0.0769 / 0.0795
+data            20060   409500  20069   409500  
+t0              20010.0 20019.0 
+
+# Bw4-Bw8 +++++++
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+alpha           33
+map            34   35   36    0    0    0    0    0    0    0    0
+forward         13 
+backward        17 
+background      500     15000   500     15000      # estimated bkg: 0.0761 / 0.0702
+data            20063   409500  20089   409500  
+t0              20013.0 20039.0 
+
+###############################################################
+COMMANDS
+#MAX_LIKELIHOOD
+PRINT_LEVEL 2
+MINIMIZE
+#MINOS
+SAVE
+
+###############################################################
+PLOT 3   (asymmetry RRF plot)
+runs     1   2   3   4   5   6   7   8   
+range    0   9.07   -0.5   0.5
+
+###############################################################
+FOURIER
+units            Gauss   # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
+fourier_power    11
+apodization      STRONG  # NONE, WEAK, MEDIUM, STRONG
+plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
+
+###############################################################
+STATISTIC --- 2016-01-18 16:23:00
+  chisq = 7402.2, NDF = 6516, chisq/NDF = 1.135997

doc/examples/test-histo-HAL9500-RRF.msr

@@ -0,0 +1,235 @@
+MnSi, FLC68.2, 50 K                                           
+###############################################################
+FITPARAMETER
+#      Nr. Name       Value     Step      Pos_Error Boundaries   
+        1 Rate_1      1.678     0.018       none        
+        2 Field_1_RRF 1589.66   0.19        none        
+        3 Rate_2      1.948     0.064       none        
+        4 Field_2_RRF 788.93    0.47        none        
+        
+        5 Asym_1      0.3102    0.0067      none        
+        6 Frc_1       0.728     0.012       none        
+        7 Phase_1     57.3      1.1         none        
+
+        8 Asym_2      0.3073    0.0066      none        
+        9 Frc_2       0.748     0.012       none        
+       10 Phase_2     30.6      1.0         none        
+
+       11 Asym_3      0.3245    0.0065      none        
+       12 Frc_3       0.728     0.011       none        
+       13 Phase_3     18.70     0.96        none        
+
+       14 Asym_4      0.3290    0.0062      none        
+       15 Frc_4       0.733     0.011       none        
+       16 Phase_4     339.27    0.96        none        
+
+       17 Asym_5      0.3213    0.0062      none        
+       18 Frc_5       0.730     0.011       none        
+       19 Phase_5     282.5     1.0         none        
+
+       20 Asym_6      0.3424    0.0072      none        
+       21 Frc_6       0.726     0.012       none        
+       22 Phase_6     211.3     1.0         none        
+
+       23 Asym_7      0.3321    0.0069      none        
+       24 Frc_7       0.731     0.012       none        
+       25 Phase_7     161.7     1.1         none        
+
+       26 Asym_8      0.3219    0.0067      none        
+       27 Frc_8       0.730     0.012       none        
+       28 Phase_8     133.7     1.1         none        
+
+       29 Asym_9      0.3030    0.0058      none        
+       30 Frc_9       0.730     0.011       none        
+       31 Phase_9     158.87    0.97        none        
+
+       32 Asym_10     0.3046    0.0057      none        
+       33 Frc_10      0.731     0.011       none        
+       34 Phase_10    129.97    0.97        none        
+
+       35 Asym_11     0.2898    0.0055      none        
+       36 Frc_11      0.754     0.011       none        
+       37 Phase_11    101.80    0.96        none        
+
+       38 Asym_12     0.3013    0.0055      none        
+       39 Frc_12      0.740     0.010       none        
+       40 Phase_12    43.00     0.88        none        
+
+       41 Asym_13     0.3009    0.0054      none        
+       42 Frc_13      0.747     0.010       none        
+       43 Phase_13    351.72    0.88        none        
+
+       44 Asym_14     0.3054    0.0053      none        
+       45 Frc_14      0.729     0.010       none        
+       46 Phase_14    289.91    0.91        none        
+
+       47 Asym_15     0.2931    0.0053      none        
+       48 Frc_15      0.740     0.010       none        
+       49 Phase_15    282.39    0.94        none        
+
+       50 Asym_16     0.2814    0.0058      none        
+       51 Frc_16      0.729     0.011       none        
+       52 Phase_16    212.89    0.99        none        
+
+###############################################################
+THEORY
+asymmetry   fun1
+simplExpo      1          (rate)
+TFieldCos   map3  fun3       (phase frequency)
++
+asymmetry   fun2
+simplExpo      3          (rate)
+TFieldCos   map3  fun4       (phase frequency)
+
+###############################################################
+FUNCTIONS
+fun1 = map1 * map2
+fun2 = map1 * (1 - map2)
+fun3 = par2 * gamma_mu
+fun4 = par4 * gamma_mu
+
+###############################################################
+GLOBAL
+fittype         1         (single histogram RRF fit)
+rrf_freq        7.15     T
+rrf_packing     300     
+rrf_phase       0.00    
+fit             0.0005  10     
+
+###############################################################
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map             5    6    7    0    0    0    0    0    0    0    0
+forward         2 
+background      100     18000      # estimated bkg: 0.0476
+data            20208   409500  
+t0              20108.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map             8    9   10    0    0    0    0    0    0    0    0
+forward         3 
+background      100     18000      # estimated bkg: 0.0490
+data            20188   409500  
+t0              20088.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            11   12   13    0    0    0    0    0    0    0    0
+forward         4 
+background      100     18000      # estimated bkg: 0.0582
+data            20161   409500  
+t0              20061.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            14   15   16    0    0    0    0    0    0    0    0
+forward         5 
+background      100     18000      # estimated bkg: 0.0553
+data            20171   409500  
+t0              20071.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            17   18   19    0    0    0    0    0    0    0    0
+forward         6 
+background      100     18000      # estimated bkg: 0.0515
+data            20180   409500  
+t0              20080.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            20   21   22    0    0    0    0    0    0    0    0
+forward         7 
+background      100     18000      # estimated bkg: 0.0458
+data            20171   409500  
+t0              20071.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            23   24   25    0    0    0    0    0    0    0    0
+forward         8 
+background      100     18000      # estimated bkg: 0.0466
+data            20166   409500  
+t0              20066.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            26   27   28    0    0    0    0    0    0    0    0
+forward         9 
+background      100     18000      # estimated bkg: 0.0457
+data            20132   409500  
+t0              20032.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            29   30   31    0    0    0    0    0    0    0    0
+forward         10 
+background      100     18000      # estimated bkg: 0.0635
+data            20122   409500  
+t0              20022.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            32   33   34    0    0    0    0    0    0    0    0
+forward         11 
+background      100     18000      # estimated bkg: 0.0685
+data            20126   409500  
+t0              20026.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            35   36   37    0    0    0    0    0    0    0    0
+forward         12 
+background      100     18000      # estimated bkg: 0.0752
+data            20110   409500  
+t0              20010.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            38   39   40    0    0    0    0    0    0    0    0
+forward         13 
+background      100     18000      # estimated bkg: 0.0760
+data            20113   409500  
+t0              20013.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            41   42   43    0    0    0    0    0    0    0    0
+forward         14 
+background      100     18000      # estimated bkg: 0.0809
+data            20117   409500  
+t0              20017.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            44   45   46    0    0    0    0    0    0    0    0
+forward         15 
+background      100     18000      # estimated bkg: 0.0755
+data            20119   409500  
+t0              20019.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            47   48   49    0    0    0    0    0    0    0    0
+forward         16 
+background      100     18000      # estimated bkg: 0.0796
+data            20119   409500  
+t0              20019.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            50   51   52    0    0    0    0    0    0    0    0
+forward         17 
+background      100     18000      # estimated bkg: 0.0702
+data            20139   409500  
+t0              20039.0 
+
+###############################################################
+COMMANDS
+#MAX_LIKELIHOOD
+PRINT_LEVEL 2
+MINIMIZE
+#MINOS
+SAVE
+
+###############################################################
+PLOT 1   (single histo RRF plot)
+runs     1   2   3   4   5   6   7   8   9   10  11  12  13  14  15  16  
+range    0   9.07   -0.5   0.5
+
+###############################################################
+FOURIER
+units            Gauss   # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
+fourier_power    12
+apodization      MEDIUM  # NONE, WEAK, MEDIUM, STRONG
+plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
+#range            7.1    7.5
+
+###############################################################
+STATISTIC --- 2016-01-14 13:24:36
+  chisq = 22007.6, NDF = 20700, chisq/NDF = 1.063168

doc/examples/test-histo-muMinus.msr

@@ -0,0 +1,199 @@
+07770 - test
+###############################################################
+FITPARAMETER
+#      Nr. Name       Value     Step      Pos_Error Boundaries   
+        1 N_0         321.0     1.4         none        
+        2 tau_0       1.9066    0.0038      none        0       none    
+        3 Rate_0      0.0983    0.0052      none        0       none    
+        4 Freq_0      135.53824 0.00073     none        
+
+        5 N_1         306.1     1.3         none        
+        6 tau_1       0.7409    0.0026      none        0       none    
+        7 Rate_1      0.026     0.027       none        0       none    
+        8 Freq_1      136.8968  0.0033      none        
+
+        9 Asym_F1_0   0.0490    0.0015      none        0       none    
+       10 Asym_F1_1   0.0501    0.0029      none        0       none    
+       11 Phase_F1    4.9       1.5         none        
+       12 N_bgk_F1    1.880     0.034       none        
+        
+       13 Asym_F2_0   0.0496    0.0015      none        0       none    
+       14 Asym_F2_1   0.0581    0.0030      none        0       none    
+       15 Phase_F2    52.4      1.5         none        
+       16 N_bgk_F2    1.508     0.033       none        
+
+       17 Asym_F3_0   0.0486    0.0015      none        0       none    
+       18 Asym_F3_1   0.0593    0.0030      none        0       none    
+       19 Phase_F3    95.2      1.5         none        
+       20 N_bgk_F3    1.465     0.033       none        
+
+       21 Asym_F4_0   0.0512    0.0015      none        0       none    
+       22 Asym_F4_1   0.0521    0.0029      none        0       none    
+       23 Phase_F4    144.6     1.5         none        
+       24 N_bgk_F4    2.311     0.034       none        
+
+       25 Asym_F5_0   0.0542    0.0015      none        0       none    
+       26 Asym_F5_1   0.0537    0.0030      none        0       none    
+       27 Phase_F5    188.4     1.4         none        
+       28 N_bgk_F5    1.799     0.033       none        
+
+       29 Asym_F6_0   0.0502    0.0015      none        0       none    
+       30 Asym_F6_1   0.0517    0.0030      none        0       none    
+       31 Phase_F6    232.1     1.5         none        
+       32 N_bgk_F6    1.735     0.033       none        
+
+       33 Asym_F7_0   0.0488    0.0015      none        0       none    
+       34 Asym_F7_1   0.0575    0.0030      none        0       none    
+       35 Phase_F7    273.0     1.5         none        
+       36 N_bgk_F7    1.593     0.033       none        
+
+       37 Asym_F8_0   0.0547    0.0015      none        0       none    
+       38 Asym_F8_1   0.0468    0.0029      none        0       none    
+       39 Phase_F8    321.7     1.4         none        
+       40 N_bgk_F8    1.469     0.033       none        
+
+       41 Asym_B1_0   0.0476    0.0015      none        0       none    
+       42 Asym_B1_1   0.0535    0.0029      none        0       none    
+       43 Phase_B1    3.6       1.5         none        
+       44 N_bgk_B1    1.378     0.033       none        
+
+       45 Asym_B2_0   0.0524    0.0015      none        0       none    
+       46 Asym_B2_1   0.0495    0.0030      none        0       none    
+       47 Phase_B2    53.7      1.5         none        
+       48 N_bgk_B2    1.272     0.032       none        
+
+       49 Asym_B3_0   0.0494    0.0015      none        0       none    
+       50 Asym_B3_1   0.0555    0.0030      none        0       none    
+       51 Phase_B3    98.1      1.5         none        
+       52 N_bgk_B3    0.969     0.032       none        
+
+       53 Asym_B4_0   0.0505    0.0015      none        0       none    
+       54 Asym_B4_1   0.0527    0.0030      none        0       none    
+       55 Phase_B4    141.8     1.5         none        
+       56 N_bgk_B4    1.233     0.032       none        
+
+       57 Asym_B5_0   0.0515    0.0015      none        0       none    
+       58 Asym_B5_1   0.0584    0.0030      none        0       none    
+       59 Phase_B5    182.2     1.4         none        
+       60 N_bgk_B5    1.642     0.033       none        
+
+       61 Asym_B6_0   0.0512    0.0015      none        0       none    
+       62 Asym_B6_1   0.0477    0.0029      none        0       none    
+       63 Phase_B6    231.7     1.5         none        
+       64 N_bgk_B6    1.650     0.033       none        
+
+       65 Asym_B7_0   0.0514    0.0015      none        0       none    
+       66 Asym_B7_1   0.0539    0.0030      none        0       none    
+       67 Phase_B7    275.2     1.5         none        
+       68 N_bgk_B7    1.729     0.033       none        
+
+       69 Asym_B8_0   0.0541    0.0015      none        0       none    
+       70 Asym_B8_1   0.0444    0.0030      none        0       none    
+       71 Phase_B8    321.0     1.5         none        
+       72 N_bgk_B8    1.136     0.032       none        
+
+###############################################################
+THEORY
+muMinusExpTF     1     2  map1     3  map3     4 (N0 tau A lambda phase nu)
++
+muMinusExpTF     5     6  map2     7  map3     8 (N0 tau A lambda phase nu)
++
+asymmetry   map4
+
+###############################################################
+GLOBAL
+fittype         4         (mu minus fit)
+t0              20000.0 
+data            20100   409500  
+fit             0.0005  9      
+packing         25
+
+###############################################################
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map             9   10   11   12    0    0    0    0    0    0    0    0
+forward         1 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            13   14   15   16    0    0    0    0    0    0    0    0
+forward         2 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            17   18   19   20    0    0    0    0    0    0    0    0
+forward         3 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            21   22   23   24    0    0    0    0    0    0    0    0
+forward         4 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            25   26   27   28    0    0    0    0    0    0    0    0
+forward         5 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            29   30   31   32    0    0    0    0    0    0    0    0
+forward         6 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            33   34   35   36    0    0    0    0    0    0    0    0
+forward         7 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            37   38   39   40    0    0    0    0    0    0    0    0
+forward         8 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            41   42   43   44    0    0    0    0    0    0    0    0
+forward         9 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            45   46   47   48    0    0    0    0    0    0    0    0
+forward         10 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            49   50   51   52    0    0    0    0    0    0    0    0
+forward         11 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            53   54   55   56    0    0    0    0    0    0    0    0
+forward         12 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            57   58   59   60    0    0    0    0    0    0    0    0
+forward         13 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            61   62   63   64    0    0    0    0    0    0    0    0
+forward         14 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            65   66   67   68    0    0    0    0    0    0    0    0
+forward         15 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            69   70   71   72    0    0    0    0    0    0    0    0
+forward         16 
+
+###############################################################
+COMMANDS
+MAX_LIKELIHOOD
+PRINT_LEVEL 2
+MINIMIZE
+#MINOS
+SAVE
+
+###############################################################
+PLOT 4   (mu minus plot)
+runs        1-16
+range    0   9
+
+###############################################################
+FOURIER
+units            Tesla   # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
+fourier_power    14
+apodization      MEDIUM  # NONE, WEAK, MEDIUM, STRONG
+plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
+range            0.8     1.2
+
+###############################################################
+STATISTIC --- 2016-04-25 17:05:56
+  maxLH = 238962.5, NDF = 230264, maxLH/NDF = 1.037776

doc/html/user/MUSR/BmwLibs.html

@@ -1,35 +1,38 @@
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+<!DOCTYPE html><html lang="en">
 
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-<title>   MUSR :: BmwLibs</title>
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+<title> MUSR :: BmwLibs</title>
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+<meta name="apple-mobile-web-app-capable" content="yes" />
+<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
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-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/BmwLibs?t=1418910336" type="application/x-wiki" title="edit BmwLibs" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/BmwLibs?t=1481904045" type="application/x-wiki" title="edit BmwLibs" />
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+<base  /><!--[if IE]></base><![endif]--><link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
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+@import url('../pub/System/PatternSkinTheme/layout.css');
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-@import url('../pub/System/PatternSkinTheme2009/variant_twiki.css');
-</style><style type="text/css" media="all">
+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/column_left.css' media='all' type='text/css' />
+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/variant_twiki.css' media='all' type='text/css' /><style type="text/css" media="all">
 	/* Styles that are set using variables */
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-	.patternWebIndicator a img,
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+	.patternWebIndicator,
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-	overflow-x:auto;
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+<link rel='stylesheet' href='../pub/System/PatternSkin/print.css' media='all' type='text/css' />
+<!--[if IE 7 ]><style type="text/css" media="screen">
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 .foswikiForm,
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@@ -79,7 +76,17 @@ pre {
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+#foswikiLogin {
+	 margin-left: 25%;
+	 margin-right: 25%;
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+#foswikiLogin .foswikiFormSteps {
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+</head> 
+<body class="foswikiNoJs patternViewPage patternPrintPage">
+<span id="PageTop"></span><div class="foswikiPage"><div id="patternScreen">
 <div id="patternPageShadow">
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+<div id="patternOuter" class="clear">
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+<div id="patternMain">
+<div id="patternMainContents">
+<div class="patternContent"><div class="foswikiTopic"> To be written...
 <p></p>
-<p></p>
-      	
-      	
-      	
-<p></p>
-<p></p>
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-<p></p>
-</div><div class="patternContent"><div class="foswikiTopic">To be written...
-<p></p>
-<h1><a name="BMWlibs_for_61musrfit_61"></a>  BMWlibs for <code>musrfit</code> </h1> <ul>
+<h1 id="BMWlibs_for_61musrfit_61">  BMWlibs for <code>musrfit</code> </h1> <ul>
 <li> <a href="LibFitPofB.html"> <code>libFitPofB</code>: routines for calculating transverse-field muon-spin depolarization functions from various static field distributions in superconductors</a>
 </li> <li> <a href="LibZFRelaxation.html"> <code>libZFRelaxation</code>: routines for calculating zero-field muon-spin depolarization functions from various static field distributions</a>
 </li></ul> 
 <p></p>
--- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> &amp; <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a> </div>
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-<!-- --><!-- -->
-<!-- --><!-- -->
-<!-- -->
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+-- <a href="http://www.fsf.org/register_form?referrer=8369">BMW</a> &amp; <a href="http://www.psi.ch/low-energy-muons/people">AS</a></div>
+<p></p>
+<p></p>
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-  </div>
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-</div>
-<p></p>
-<p></p>
-<b>PSI Webs</b> <ul>
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-</li> <li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/psi.png" width="16" height="16" alt="psi" /></span> <a href="https://intranet.psi.ch/Main/WebList">weitere Webs</a>
-</li></ul> 
-<hr />
-<b>System Webs</b> <ul>
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-</li></ul> 
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-</li> <li> <form name="changeLanguage"    action="https://intranet.psi.ch/wiki/bin/oops/MUSR/BmwLibs" method="get">    <input type="hidden" name="redirectto" value="/MUSR/BmwLibs?cover=print" />    <select name="language" class="foswikiSelect"        onchange="document.changeLanguage.submit()">    <option  value="de">Deutsch</option> <option selected="selected" value="en">English</option></select>    <input type="hidden" name="template" value="oopslanguagechanged" />    <noscript>        <input class="foswikiButton" type="submit"            value="Change language" />    </noscript> </form>
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+<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span><a class="foswikiCurrentWebHomeLink" href="WebHome.html">WebHome</a> &gt; <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>BmwLibs <br />
+Topic revision:  <span class='patternRevInfo'>03 Jul 2015, suter_a</span></div>
 </div>
 </div>
 </div>
-</div></body>
-<!-- Mirrored from intranet.psi.ch/MUSR/BmwLibs?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 18 Dec 2014 13:46:47 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=iso-8859-1"><!-- /Added by HTTrack -->
-</html>
+</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar"><span class="foswikiRight"> <a href="http://foswiki.org/"><img src="../pub/System/ProjectLogos/foswiki-badge.png" alt="This site is powered by Foswiki" title="This site is powered by Foswiki" /></a></span>Copyright &copy; by the contributing authors. All material on this collaboration platform is the property of the contributing authors. <br /> Ideas, requests, problems regarding PSI Wiki? <a href='mailto:thomas.buecklers@psi.ch?subject=PSI Wiki %20Feedback%20on%20MUSR.BmwLibs'>Send feedback</a></div></div></div>
+</div>
+</div>
+</div>
+</div></div><!-- /endWrap -->
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+<!-- Piwik -->
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+<!-- Mirrored from intranet.psi.ch/MUSR/BmwLibs?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:33 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+</html>

doc/html/user/MUSR/CiteMusrFit.html

@@ -1,35 +1,38 @@
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+<!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/CiteMusrFit?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 18 Dec 2014 13:46:34 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=iso-8859-1"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/CiteMusrFit?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:25 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
 <head>
 <link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
-<title>   MUSR :: CiteMusrFit</title>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+<title> MUSR :: CiteMusrFit</title>
+<meta http-equiv="X-UA-Compatible" content="IE=edge" />
+<meta charset="utf-8" />
+<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1.5, user-scalable=yes" />
+<meta name="mobile-web-app-capable" content="yes" />
+<meta name="mobile-web-app-status-bar-style" content="black-translucent" />
+<meta name="apple-mobile-web-app-capable" content="yes" />
+<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
 <link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
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-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/CiteMusrFit?t=1418910332" type="application/x-wiki" title="edit CiteMusrFit" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/CiteMusrFit?t=1481904044" type="application/x-wiki" title="edit CiteMusrFit" />
 <meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
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-<base  /><!--[if IE]></base><![endif]-->
-<link rel='stylesheet' href='../pub/System/ImagePlugin/style.css' media='all' />
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+<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
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+@import url('../pub/System/PatternSkinTheme/layout.css');
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-@import url('../pub/System/PatternSkinTheme2009/variant_twiki.css');
-</style><style type="text/css" media="all">
+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/column_left.css' media='all' type='text/css' />
+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/variant_twiki.css' media='all' type='text/css' /><style type="text/css" media="all">
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-</div><div class="patternContent"><div class="foswikiTopic"><h1><a name="How_to_Cite_61musrfit_61_63"></a>  How to Cite <code>musrfit</code>? </h1>
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+<div id="patternMainContents">
+<div class="patternContent"><div class="foswikiTopic"> <h1 id="How_to_Cite_61musrfit_61_63">  How to Cite <code>musrfit</code>? </h1>
 <p></p>
 Since quite some effort is going into the development and maintenance of the <code>musrfit</code> package, you should at least acknowledge it in your publication if you have used it to analyze your data. Even better of course is to cite it properly by the reference given beneath 
 <p></p> <ul>
-<li>  <a href="http://dx.doi.org/10.1016/j.phpro.2012.04.042" target="_top">A. Suter, B.M. Wojek, "Musrfit: A Free Platform-Independent Framework for &mu;SR Data Analysis", Physics Procedia 30, 69 (2012).</a>
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+<li>  <a href="http://dx.doi.org/10.1016/j.phpro.2012.04.042">A. Suter, B.M. Wojek, "Musrfit: A Free Platform-Independent Framework for &mu;SR Data Analysis", Physics Procedia 30, 69 (2012).</a>
+</li></ul> </div>
+<p></p>
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-  </div>
-</div></div><div class="patternInfo"><span class="patternRevInfo">Topic revision: r2 - 19 Jun 2012, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
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+<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span><a class="foswikiCurrentWebHomeLink" href="WebHome.html">WebHome</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>CiteMusrFit <br />
+Topic revision:  <span class='patternRevInfo'>19 Jun 2012, suter_a</span></div>
 </div>
 </div>
 </div>
-</div></body>
-<!-- Mirrored from intranet.psi.ch/MUSR/CiteMusrFit?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 18 Dec 2014 13:46:35 GMT -->
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+</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar"><span class="foswikiRight"> <a href="http://foswiki.org/"><img src="../pub/System/ProjectLogos/foswiki-badge.png" alt="This site is powered by Foswiki" title="This site is powered by Foswiki" /></a></span>Copyright &copy; by the contributing authors. All material on this collaboration platform is the property of the contributing authors. <br /> Ideas, requests, problems regarding PSI Wiki? <a href='mailto:thomas.buecklers@psi.ch?subject=PSI Wiki %20Feedback%20on%20MUSR.CiteMusrFit'>Send feedback</a></div></div></div>
+</div>
+</div>
+</div>
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+<!-- Mirrored from intranet.psi.ch/MUSR/CiteMusrFit?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:25 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+</html>

doc/html/user/MUSR/LibFitPofB.html

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+<!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/LibFitPofB?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 18 Dec 2014 13:46:37 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=iso-8859-1"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/LibFitPofB?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:26 GMT -->
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+<title> MUSR :: LibFitPofB</title>
+<meta http-equiv="X-UA-Compatible" content="IE=edge" />
+<meta charset="utf-8" />
+<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1.5, user-scalable=yes" />
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+<meta name="apple-mobile-web-app-capable" content="yes" />
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+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/LibFitPofB?t=1481904045" type="application/x-wiki" title="edit LibFitPofB" />
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+@import url('../pub/System/PatternSkinTheme/layout.css');
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+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/column_left.css' media='all' type='text/css' />
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+<div class="foswikiToc" id="foswikiTOC"> <ul>
 <li> <a href="LibFitPofB.html#libFitPofB"> libFitPofB </a>
 </li> <li> <a href="LibFitPofB.html#A_1_Introduction"> 1  Introduction </a>
 </li> <li> <a href="LibFitPofB.html#A_2_LE_45SR"> 2  LE-&mu;SR </a> <ul>
@@ -130,28 +137,28 @@ pre {
 </li> <li> <a href="LibFitPofB.html#A_4_The_XML_startup_file"> 4  The XML startup file </a>
 </li></ul> 
 </div>
-<a name="IntroDuction"></a>
-<h1><a name="A_1_Introduction"></a> 1  Introduction </h1>
+<span id="IntroDuction"></span>
+<h1 id="A_1_Introduction"> 1  Introduction </h1>
 <p></p>
 <code>libFitPofB</code> is a collection of <code>C++</code> classes using the <code><a href="MusrFit.html">musrfit</a></code> <code><a href="MusrFit.html#UserFunctions1">user-function interface</a></code> in order to facilitate the usage in conjunction with <code>musrfit</code>. The classes contained in this library generally implement calculations of one-dimensional static magnetic field distributions <img alt="P(B)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_9cc0fd47eedada7247b14775bd308deb.png" title="PofB" /> which lead to muon-spin depolarization functions
 <p style="text-align:center">
 <img alt="\mathcal{P}(t) &#61; \int P(B)\cos\left(\gamma&#95;{\mu} B t + \varphi\right) \mathrm{d}B," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_70e57aa1afa7d337fa46f427b34feb54.png" title="PofT" />
 </p>
 where <img alt="\gamma&#95;{\mu} &#61; 2\pi\times 135.54~\mathrm{MHz/T}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_9bb7e08c8e276a92650d89d6918b3769.png" title="gamma_mu" /> is the gyromagnetic ratio of the muon and <img alt="\varphi" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_2339fd9b358ebe241da05c665668d48b.png" title="phi" /> is the initial phase of the muon spins with respect to the positron detector.<br>
-At the moment the only available implementations deal with field distributions measured in local isotropic superconductors, either by means of <a href="http://lmu.web.psi.ch/lem/" target="_top">low-energy &mu;SR</a> in the Meissner state or by conventional &mu;SR in the mixed state. In the following the basic usage of the library in <code>musrfit</code> is explained&mdash;the calculations by themselves are only outlined. For further information please refer to the original literature and/or the source code of the implementation.
+At the moment the only available implementations deal with field distributions measured in local isotropic superconductors, either by means of <a href="http://lmu.web.psi.ch/lem/">low-energy &mu;SR</a> in the Meissner state or by conventional &mu;SR in the mixed state. In the following the basic usage of the library in <code>musrfit</code> is explained&mdash;the calculations by themselves are only outlined. For further information please refer to the original literature and/or the source code of the implementation.
 <p></p>
 <hr />
-<strong><span class='foswikiBlackFG'>Remark 1:</span></strong> In order to supply certain information needed for the calculations but not suited to be stored in the <code>musrfit</code> msr files an XML configuration file in the working directory is used. For details, see <a href="#XmlFile" class="foswikiCurrentTopicLink">below</a>.
+<strong><span class='foswikiBlackFG'>Remark 1:</span></strong> In order to supply certain information needed for the calculations but not suited to be stored in the <code>musrfit</code> msr files an XML configuration file in the working directory is used. For details, see <a class="foswikiCurrentTopicLink" href="#XmlFile">below</a>.
 <p></p>
-<strong><span class='foswikiBlackFG'>Remark 2:</span></strong> The implementations in this library heavily rely on <code><a href="http://www.fftw.org/" target="_top">FFTW3</a></code>. In principle, it always checks what is the best way to do efficient Fourier transforms for a given machine before the transforms are actually done. If repeatedly Fourier transforms of the same (sizable) length should be done, it might be worth storing the once obtained information in an external file and just load it the next time this information is needed (<a href="http://fftw.org/fftw3_doc/Wisdom.html" target="_top">"wisdom handling"</a>). In case this feature shall be used, a valid wisdom file has to be specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML file</a>.
+<strong><span class='foswikiBlackFG'>Remark 2:</span></strong> The implementations in this library heavily rely on <code><a href="http://www.fftw.org/">FFTW3</a></code>. In principle, it always checks what is the best way to do efficient Fourier transforms for a given machine before the transforms are actually done. If repeatedly Fourier transforms of the same (sizable) length should be done, it might be worth storing the once obtained information in an external file and just load it the next time this information is needed (<a href="http://fftw.org/fftw3_doc/Wisdom.html">"wisdom handling"</a>). In case this feature shall be used, a valid wisdom file has to be specified in the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML file</a>.
 <p></p>
 <strong><span class='foswikiBlackFG'>Remark 3:</span></strong> The model functions described in the following do generally not behave nicely in conjunction with <code>MINUIT</code> function minimizations (or maximizations). The analysis process at the moment in most cases involves some tedious <em>trial-and-error</em> procedure, where the displayed <code>MINUIT</code> information as always deserves attention. This is especially true if small effects should be analyzed (e.g. small diamagnetic shifts in superconductors). The parameter uncertainty in many cases has to be estimated independently. Due to these limitations, also the use of the fit option of <code><a href="Msr2Data.html">msr2data</a></code> cannot be advised.
 <p></p>
 <strong><span class='foswikiBlackFG'>Remark 4:</span></strong> If these classes still prove useful and results obtained through them are part of scientific publications,
 an acknowledgement of the use of the library is appreciated.
 <p></p>
-<h1><a name="A_2_LE_45SR"></a> 2  LE-&mu;SR </h1>
-<h2><a name="A_2.1_One_45dimensional_London_model_for_the_Meissner_state_of_isotropic_superconductors"></a> 2.1  One-dimensional London model for the Meissner state of isotropic superconductors </h2>
+<h1 id="A_2_LE_45SR"> 2  LE-&mu;SR </h1>
+<h2 id="A_2.1_One_45dimensional_London_model_for_the_Meissner_state_of_isotropic_superconductors"> 2.1  One-dimensional London model for the Meissner state of isotropic superconductors </h2>
 <p></p>
 The models for analyzing LE-&mu;SR data assume the magnetic induction <img alt="B(z)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_532f98969690650ac4d127919a0eda38.png" title="BofZ" /> to vary only in the dimension parallel to the momentum of the incident muons. In such a case the magnetic field distribution is given by
 <p style="text-align:center">
@@ -163,7 +170,7 @@ Assuming an array of <img alt="N" class="mmpImage" src="../pub/MUSR/LibFitPofB/_
 <p style="text-align:center">
 <img alt="\frac{\partial^2}{\partial z^2}B&#95;i(z) &#61; \frac{1}{\lambda&#95;i^2}B&#95;i(z)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_dfd02951094e1cb98f48e3f6d4562f38.png" title="London-eq" />
 </p>
-for each layer <img alt="i" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_c465118a8d86d5f25bba37cc1dcb38a0.png" title="i" /> taking into account the boundary conditions<a name="FootNote1text"></a><span class='FootNoteTextLink' title='F. London, Superfluids: Macroscopic Theory of Superconductivity, Dover (1961), p. 34'><a href="#FootNote1note" class="foswikiCurrentTopicLink">(1)</a></span>
+for each layer <img alt="i" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_c465118a8d86d5f25bba37cc1dcb38a0.png" title="i" /> taking into account the boundary conditions<a name="FootNote1text"></a><span class="FootNoteTextLink" title="F&#46; London&#44; Superfluids&#58; Macroscopic Theory of Superconductivity&#44; Dover &#40;1961&#41;&#44; p&#46; 34"><a class="foswikiCurrentTopicLink" href="#FootNote1note">(1)</a></span>
 <p style="text-align:center">
 <img alt="B&#95;1(0) &#61; B&#95;N(d) &#61; \mu&#95;0H" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_432d7664e0756ded77e7423dd256c122.png" title="cond1" />
 </p>
@@ -182,19 +189,19 @@ userFcn  libFitPofB TLondon1DHS 1 2 3 4 5
 </dd></dl> 
 The parameters are: <ol>
 <li> phase (deg)
-</li> <li> muon implantation energy as specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML startup file</a> (keV)
+</li> <li> muon implantation energy as specified in the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML startup file</a> (keV)
 </li> <li> applied field (G)
 </li> <li> thickness of the dead layer (nm)
 </li> <li> magnetic field penetration depth (nm) 
 </li></ol> 
 <p></p> <dl>
 <dt> Superconducting thin film (one layer) </dt><dd> <pre>
-userFcn  libFitPofB TLondon1D1L 1 2 3 4 5 6 &#91;a b]
+userFcn  libFitPofB TLondon1D1L 1 2 3 4 5 6 &#91;a b&#93;
 </pre>
 </dd></dl> 
 The mandatory parameters are: <ol>
 <li> phase (deg)
-</li> <li> muon implantation energy as specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML startup file</a> (keV)
+</li> <li> muon implantation energy as specified in the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML startup file</a> (keV)
 </li> <li> applied field (G)
 </li> <li> thickness of the dead layer (nm)
 </li> <li> thickness of the actually superconducting layer (nm)
@@ -202,17 +209,17 @@ The mandatory parameters are: <ol>
 </li></ol> 
 <p></p>
 The optional parameters are: <ol>
-<li type="a"> fraction <i>f</i><sub>1</sub> of muons in the thin film contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1)
-</li> <li type="a"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1)
+<li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>1</sub> of muons in the thin film contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1)
+</li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1)
 </li></ol> 
 <p></p> <dl>
 <dt> Superconducting thin-film bilayer heterostructure </dt><dd> <pre>
-userFcn  libFitPofB TLondon1D2L 1 2 3 4 5 6 7 8 &#91;a b c]
+userFcn  libFitPofB TLondon1D2L 1 2 3 4 5 6 7 8 &#91;a b c&#93;
 </pre>
 </dd></dl> 
 The mandatory parameters are: <ol>
 <li> phase (deg)
-</li> <li> muon implantation energy as specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML startup file</a> (keV)
+</li> <li> muon implantation energy as specified in the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML startup file</a> (keV)
 </li> <li> applied field (G)
 </li> <li> thickness of the dead layer (nm)
 </li> <li> thickness of the actually superconducting first layer (nm)
@@ -222,18 +229,18 @@ The mandatory parameters are: <ol>
 </li></ol> 
 <p></p>
 The optional parameters are: <ol>
-<li type="a"> fraction <i>f</i><sub>1</sub> of muons in the dead and first layer contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1)
-</li> <li type="a"> fraction <i>f</i><sub>2</sub> of muons in the second layer contributing to the signal (0 &le; <i>f</i><sub>2</sub> &le; 1)
-</li> <li type="a"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1)
+<li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>1</sub> of muons in the dead and first layer contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1)
+</li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>2</sub> of muons in the second layer contributing to the signal (0 &le; <i>f</i><sub>2</sub> &le; 1)
+</li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1)
 </li></ol> 
 <p></p> <dl>
 <dt> Superconducting thin-film trilayer heterostructure </dt><dd> <pre>
-userFcn  libFitPofB TLondon1D3L 1 2 3 4 5 6 7 8 9 10 &#91;a b c d]
+userFcn  libFitPofB TLondon1D3L 1 2 3 4 5 6 7 8 9 10 &#91;a b c d&#93;
 </pre>
 </dd></dl> 
 The mandatory parameters are: <ol>
 <li> phase (deg)
-</li> <li> muon implantation energy as specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML startup file</a> (keV)
+</li> <li> muon implantation energy as specified in the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML startup file</a> (keV)
 </li> <li> applied field (G)
 </li> <li> thickness of the dead layer (nm)
 </li> <li> thickness of the actually superconducting first layer (nm)
@@ -245,39 +252,39 @@ The mandatory parameters are: <ol>
 </li></ol> 
 <p></p>
 The optional parameters are: <ol>
-<li type="a"> fraction <i>f</i><sub>1</sub> of muons in the dead and first layer contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1)
-</li> <li type="a"> fraction <i>f</i><sub>2</sub> of muons in the second layer contributing to the signal (0 &le; <i>f</i><sub>2</sub> &le; 1)
-</li> <li type="a"> fraction <i>f</i><sub>3</sub> of muons in the third layer contributing to the signal (0 &le; <i>f</i><sub>3</sub> &le; 1)
-</li> <li type="a"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1)
+<li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>1</sub> of muons in the dead and first layer contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1)
+</li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>2</sub> of muons in the second layer contributing to the signal (0 &le; <i>f</i><sub>2</sub> &le; 1)
+</li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>3</sub> of muons in the third layer contributing to the signal (0 &le; <i>f</i><sub>3</sub> &le; 1)
+</li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1)
 </li></ol> 
 <p></p>
 <p></p>
 <p></p>
 Notes
 <p></p>
-<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="#FootNote1text" class="foswikiCurrentTopicLink"> <strong>1</strong> </a></span>: <span class="FootNote">F. London, Superfluids: Macroscopic Theory of Superconductivity, Dover (1961), p. 34</span> 
+<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="#FootNote1text"><b>1</b></a></span>: <span class="FootNote">F. London, Superfluids: Macroscopic Theory of Superconductivity, Dover (1961), p. 34</span> 
 <p></p>
 <p></p>
 <p></p>
 <hr />
 <p></p>
-<h1><a name="A_3_Conventional_40bulk_41_SR"></a> 3  Conventional (bulk) &mu;SR </h1>
-<h2><a name="A_3.1_Field_distributions_in_the_mixed_state_of_isotropic_superconductors"></a> 3.1  Field distributions in the mixed state of isotropic superconductors </h2>
+<h1 id="A_3_Conventional_40bulk_41_SR"> 3  Conventional (bulk) &mu;SR </h1>
+<h2 id="A_3.1_Field_distributions_in_the_mixed_state_of_isotropic_superconductors"> 3.1  Field distributions in the mixed state of isotropic superconductors </h2>
 <p></p>
 When investigating superconductors in the mixed state by means of conventional &mu;SR a two-dimensional flux-line lattice is probed randomly by the muons. The spatial field distributions within such an ordered lattice are modeled using the Fourier series
 <p style="text-align:center">
 <img alt="B(\mathbf{r}) &#61; \langle B \rangle \sum\limits&#95;{\mathbf{K}}B&#95;{\mathbf{K}}\exp(-\imath\mathbf{K}\mathbf{r})," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_c25933e91d56089992506f463d71de8f.png" title="spatialB" />
 </p>
 where <img alt="\mathbf{r}&#61;(x,y)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e47f33589d28eaa3f9baccb7a80fdbaa.png" title="r" />, <img alt="\mathbf{K}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e6688a12ee4e821abc31b4c1dd511539.png" title="K" /> are the reciprocal lattice vectors of a two-dimensional vortex lattice and the <img alt="B&#95;{\mathbf{K}}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_8fa3ac8f18b7bc49eb89163d6528684c.png" title="Bk" /> are the Fourier coefficients depending on the magnetic penetration depth <img alt="\lambda" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_28f3ed750a4819b4256c2f9be649f594.png" title="lambda" /> and the superconducting coherence length <img alt="\xi" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e8414d477977d226317c020980b7d34f.png" title="xi" />. The <img alt="B&#95;{\mathbf{K}}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_8fa3ac8f18b7bc49eb89163d6528684c.png" title="Bk" /> for some specific models are as follows: <dl>
-<dt> London model with Gaussian cutoff<a name="FootNote2text"></a><span class='FootNoteTextLink' title='E.H. Brandt, <a href="http://dx.doi.org/10.1007/BF00683568" target="_top">J. Low Temp. Phys. <strong>73</strong>, 355 (1988)</a>.'><a href="#FootNote2note" class="foswikiCurrentTopicLink">(2)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{\exp\left({-K^2\xi^2/2}\right)}{1 + K^2\lambda^2}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_469d5d1b83125e4915e2f073d8150b12.png" title="BkLondon" /></p>
-</dd> <dt> Modified London model<a name="FootNote3text"></a><span class='FootNoteTextLink' title='T.M. Riseman <em>et al.</em>, <a href="http://dx.doi.org/10.1103/PhysRevB.52.10569" target="_top">Phys. Rev. B <strong>52</strong>, 10569 (1995)</a>.'><a href="#FootNote3note" class="foswikiCurrentTopicLink">(3)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{\exp\left({-K^2\xi^2/2(1-b)}\right)}{1 + K^2\lambda^2/(1-b)}," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_b6719fad8e30208538b34bc94040b7a5.png" title="BkML" /></p> where <img alt="b &#61; \langle B \rangle/\mu&#95;0H&#95;{\mathrm{c}2}." class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_039b3b38df7c6f284089c14f1efdf643.png" title="b" />
-</dd> <dt> Analytical Ginzburg-Landau model<a name="FootNote4text"></a><span class='FootNoteTextLink' title='A. Yaouanc, P. Dalmas de R&eacute;otier and E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.55.11107" target="_top">Phys. Rev. B <strong>55</strong>, 11107 (1997)</a>.'><a href="#FootNote4note" class="foswikiCurrentTopicLink">(4)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{f&#95;{\infty}K&#95;1\left(\frac{\xi&#95;v}{\lambda}\sqrt{f&#95;{\infty}^2+\lambda^2K^2}\right)}{K&#95;1\left(\frac{\xi&#95;v}{\lambda}f&#95;{\infty}\right)\sqrt{f&#95;{\infty}^2+\lambda^2K^2}}," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_3146cb17887e3a20cc2078f103605af5.png" title="BkAGL" /></p> where <img alt="f&#95;{\infty} &#61; 1 - b^4,~\xi&#95;v &#61; \xi\left(\sqrt{2}-{3\xi}/\left({4\lambda}\right)\right)\sqrt{(1+b^4)(1-2b(1-b)^2)}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e0b0e98f9a3974249b42b6910523c8a4.png" title="f_inf_and_xi_v" /> and <img alt="K&#95;1" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_3cee3cc69dbe918398ec39a72a465014.png" title="K1" /> is a modified Bessel function.
+<dt> London model with Gaussian cutoff<a name="FootNote2text"></a><span class="FootNoteTextLink" title="E&#46;H&#46; Brandt&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1007&#47;BF00683568&#93;&#91;J&#46; Low Temp&#46; Phys&#46; &#42;73&#42;&#44; 355 &#40;1988&#41;&#93;&#93;&#46;"><a class="foswikiCurrentTopicLink" href="#FootNote2note">(2)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{\exp\left({-K^2\xi^2/2}\right)}{1 + K^2\lambda^2}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_469d5d1b83125e4915e2f073d8150b12.png" title="BkLondon" /></p>
+</dd> <dt> Modified London model<a name="FootNote3text"></a><span class="FootNoteTextLink" title="T&#46;M&#46; Riseman _et al&#46;_&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1103&#47;PhysRevB&#46;52&#46;10569&#93;&#91;Phys&#46; Rev&#46; B &#42;52&#42;&#44; 10569 &#40;1995&#41;&#93;&#93;&#46;"><a class="foswikiCurrentTopicLink" href="#FootNote3note">(3)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{\exp\left({-K^2\xi^2/2(1-b)}\right)}{1 + K^2\lambda^2/(1-b)}," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_b6719fad8e30208538b34bc94040b7a5.png" title="BkML" /></p> where <img alt="b &#61; \langle B \rangle/\mu&#95;0H&#95;{\mathrm{c}2}." class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_039b3b38df7c6f284089c14f1efdf643.png" title="b" />
+</dd> <dt> Analytical Ginzburg-Landau model<a name="FootNote4text"></a><span class="FootNoteTextLink" title="A&#46; Yaouanc&#44; P&#46; Dalmas de R&#38;eacute&#59;otier and E&#46;H&#46; Brandt&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1103&#47;PhysRevB&#46;55&#46;11107&#93;&#91;Phys&#46; Rev&#46; B &#42;55&#42;&#44; 11107 &#40;1997&#41;&#93;&#93;&#46;"><a class="foswikiCurrentTopicLink" href="#FootNote4note">(4)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{f&#95;{\infty}K&#95;1\left(\frac{\xi&#95;v}{\lambda}\sqrt{f&#95;{\infty}^2+\lambda^2K^2}\right)}{K&#95;1\left(\frac{\xi&#95;v}{\lambda}f&#95;{\infty}\right)\sqrt{f&#95;{\infty}^2+\lambda^2K^2}}," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_3146cb17887e3a20cc2078f103605af5.png" title="BkAGL" /></p> where <img alt="f&#95;{\infty} &#61; 1 - b^4,~\xi&#95;v &#61; \xi\left(\sqrt{2}-{3\xi}/\left({4\lambda}\right)\right)\sqrt{(1+b^4)(1-2b(1-b)^2)}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e0b0e98f9a3974249b42b6910523c8a4.png" title="f_inf_and_xi_v" /> and <img alt="K&#95;1" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_3cee3cc69dbe918398ec39a72a465014.png" title="K1" /> is a modified Bessel function.
 </dd></dl> 
-Apart from the mentioned analytical models the <strong>numerical Ginzburg-Landau model</strong> <a name="FootNote5text"></a><span class='FootNoteTextLink' title='E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.68.054506" target="_top">Phys. Rev. B <strong>68</strong>, 054506 (2003)</a>.'><a href="#FootNote5note" class="foswikiCurrentTopicLink">(5)</a></span> is available. In this case <img alt="B(\mathbf{r})" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_373e9bf1fc97e2c6aacf93bcc090402c.png" title="BofR" /> is obtained by an iterative minimization of the free energy of the vortex lattice.
+Apart from the mentioned analytical models the <strong>numerical Ginzburg-Landau model</strong> <a name="FootNote5text"></a><span class="FootNoteTextLink" title="E&#46;H&#46; Brandt&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1103&#47;PhysRevB&#46;68&#46;054506&#93;&#91;Phys&#46; Rev&#46; B &#42;68&#42;&#44; 054506 &#40;2003&#41;&#93;&#93;&#46;"><a class="foswikiCurrentTopicLink" href="#FootNote5note">(5)</a></span> is available. In this case <img alt="B(\mathbf{r})" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_373e9bf1fc97e2c6aacf93bcc090402c.png" title="BofR" /> is obtained by an iterative minimization of the free energy of the vortex lattice.
 <p></p>
 <span class='foswikiRedFG'>Concerning the applicability (e.g. field regions) of each of the mentioned models please refer to the original publications!</span>
 <p></p>
-At the moment, the calculation of the field distribution has been implemented for triangular flux-line lattices. The number of grid lines in which the inter-vortex distance is divided for the calculations to be specified through the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML file</a>.<br>The muon-spin depolarization functions finally are calculated using the following lines in the THEORY block of a <code>musrfit</code> msr file: <dl>
+At the moment, the calculation of the field distribution has been implemented for triangular flux-line lattices. The number of grid lines in which the inter-vortex distance is divided for the calculations to be specified through the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML file</a>.<br>The muon-spin depolarization functions finally are calculated using the following lines in the THEORY block of a <code>musrfit</code> msr file: <dl>
 <dt> 2D triangular vortex lattice, London model with Gaussian cutoff </dt><dd> <pre>
 userFcn  libFitPofB TBulkTriVortexLondon 1 2 3 4
 </pre>
@@ -336,23 +343,23 @@ SAVE
 <p></p>
 Notes
 <p></p>
-<a name="FootNote2note"></a><span class="FootNoteLabel"><a href="#FootNote2text" class="foswikiCurrentTopicLink"> <strong>2</strong> </a></span>: <span class="FootNote">E.H. Brandt, <a href="http://dx.doi.org/10.1007/BF00683568" target="_top">J. Low Temp. Phys. <strong>73</strong>, 355 (1988)</a>.</span> 
+<a name="FootNote2note"></a><span class="FootNoteLabel"><a href="#FootNote2text"><b>2</b></a></span>: <span class="FootNote">E.H. Brandt, <a href="http://dx.doi.org/10.1007/BF00683568">J. Low Temp. Phys. <strong>73</strong>, 355 (1988)</a>.</span> 
 <p></p>
-<a name="FootNote3note"></a><span class="FootNoteLabel"><a href="#FootNote3text" class="foswikiCurrentTopicLink"> <strong>3</strong> </a></span>: <span class="FootNote">T.M. Riseman <em>et al.</em>, <a href="http://dx.doi.org/10.1103/PhysRevB.52.10569" target="_top">Phys. Rev. B <strong>52</strong>, 10569 (1995)</a>.</span> 
+<a name="FootNote3note"></a><span class="FootNoteLabel"><a href="#FootNote3text"><b>3</b></a></span>: <span class="FootNote">T.M. Riseman <em>et al.</em>, <a href="http://dx.doi.org/10.1103/PhysRevB.52.10569">Phys. Rev. B <strong>52</strong>, 10569 (1995)</a>.</span> 
 <p></p>
-<a name="FootNote4note"></a><span class="FootNoteLabel"><a href="#FootNote4text" class="foswikiCurrentTopicLink"> <strong>4</strong> </a></span>: <span class="FootNote">A. Yaouanc, P. Dalmas de R&eacute;otier and E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.55.11107" target="_top">Phys. Rev. B <strong>55</strong>, 11107 (1997)</a>.</span> 
+<a name="FootNote4note"></a><span class="FootNoteLabel"><a href="#FootNote4text"><b>4</b></a></span>: <span class="FootNote">A. Yaouanc, P. Dalmas de R&eacute;otier and E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.55.11107">Phys. Rev. B <strong>55</strong>, 11107 (1997)</a>.</span> 
 <p></p>
-<a name="FootNote5note"></a><span class="FootNoteLabel"><a href="#FootNote5text" class="foswikiCurrentTopicLink"> <strong>5</strong> </a></span>: <span class="FootNote">E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.68.054506" target="_top">Phys. Rev. B <strong>68</strong>, 054506 (2003)</a>.</span> 
+<a name="FootNote5note"></a><span class="FootNoteLabel"><a href="#FootNote5text"><b>5</b></a></span>: <span class="FootNote">E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.68.054506">Phys. Rev. B <strong>68</strong>, 054506 (2003)</a>.</span> 
 <p></p>
 <p></p>
 <p></p>
 <hr />
 <p></p>
-<a name="XmlFile"></a>
-<h1><a name="A_4_The_XML_startup_file"></a> 4  The XML startup file </h1>
+<span id="XmlFile"></span>
+<h1 id="A_4_The_XML_startup_file"> 4  The XML startup file </h1>
 <code><b>BMW_startup.xml</b></code> is a configuration file located in the working directory. In this file some settings like the time and field resolution of the calculations as well as the present muon implantation profiles for a LE-&mu;SR analysis have to be defined. The following XML tags are allowed to define settings: <dl>
 <dt> &lt;debug&gt;ONE_OR_ZERO&lt;/debug&gt; </dt><dd> activate the debugging output of the settings read from the XML file by setting <strong>1</strong>, deactivate it with <strong>0</strong>
-</dd> <dt> &lt;wisdom&gt;PATH_TO_FILE&lt;/wisdom&gt; </dt><dd> specify the <strong>PATH_TO_FILE</strong> to an <a href="http://fftw.org/fftw3_doc/Wisdom.html#Wisdom" target="_top">FFTW3 wisdom file</a> that should be used; if the <strong>PATH_TO_FILE</strong> is invalid, no FFTW3 wisdom will be used
+</dd> <dt> &lt;wisdom&gt;PATH_TO_FILE&lt;/wisdom&gt; </dt><dd> specify the <strong>PATH_TO_FILE</strong> to an <a href="http://fftw.org/fftw3_doc/Wisdom.html#Wisdom">FFTW3 wisdom file</a> that should be used; if the <strong>PATH_TO_FILE</strong> is invalid, no FFTW3 wisdom will be used
 </dd> <dt> &lt;delta_t&gt;ResT&lt;/delta_t&gt; </dt><dd> set the time resolution <strong>ResT</strong> for the calculated depolarization function in <strong>microseconds</strong>
 </dd> <dt> &lt;delta_B&gt;ResB&lt;/delta_B&gt; </dt><dd> set the field resolution <strong>ResB</strong> for the calculated field distribution in <strong>Gauss</strong>
 </dd> <dt> &lt;VortexLattice&gt;&lt;/VortexLattice&gt; </dt><dd> set the parameters used for the calculation of the spatial field distribution of a vortex lattice <dl>
@@ -398,83 +405,29 @@ An example XML file looks as follows:
 &#60;/BMW&#62;
 </pre>
 <p></p>
--- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> &amp; <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a> </div>
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doc/html/user/MUSR/LibZFRelaxation.html

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+<!DOCTYPE html><html lang="en">
 
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-<title>   MUSR :: LibZFRelaxation</title>
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+<title> MUSR :: LibZFRelaxation</title>
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+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/LibZFRelaxation?t=1481904042" type="application/x-wiki" title="edit LibZFRelaxation" />
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+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/column_left.css' media='all' type='text/css' />
+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/variant_twiki.css' media='all' type='text/css' /><style type="text/css" media="all">
 	/* Styles that are set using variables */
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-	.patternWebIndicator a img,
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@@ -50,14 +53,8 @@
 	
 
 
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-</style>
-<!--[if IE]><style type="text/css" media="screen">
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+<link rel='stylesheet' href='../pub/System/PatternSkin/print.css' media='all' type='text/css' />
+<!--[if IE 7 ]><style type="text/css" media="screen">
 .foswikiAttachments,
 .foswikiForm,
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@@ -79,7 +76,17 @@ pre {
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+#foswikiLogin {
+	 margin-left: 25%;
+	 margin-right: 25%;
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-<div id="patternMainContents"><div class="patternTop"><span class="patternHomePath foswikiLeft"></span><span class="patternToolBar foswikiRight"><span><a href='LibZFRelaxationc99a.html?cover=print;cover=print' rel='nofollow' title='Printable version of this topic' accesskey='p'><span class='foswikiAccessKey'>P</span>rint version</a></span><a href="https://intranet.psi.ch/MUSR/LibZFRelaxation?restrictions=on" id="restriction_link"><img src='../pub/System/PsiSkin/lock_open.png' class='lock' height='16' width='23' title='open in PSI - click for more information'/></a></span><div class="foswikiClear"></div></div><div class="foswikiContentHeader">
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-<a name="TopIc"></a>
-<h1><a name="libZFRelaxation"></a>  libZFRelaxation </h1>
-<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
+<div id="patternMain">
+<div id="patternMainContents">
+<div class="patternContent"><div class="foswikiTopic"> 
+<span id="TopIc"></span>
+<h1 id="libZFRelaxation">  libZFRelaxation </h1>
+<div class="foswikiToc" id="foswikiTOC"> <ul>
 <li> <a href="LibZFRelaxation.html#libZFRelaxation"> libZFRelaxation </a>
 </li> <li> <a href="LibZFRelaxation.html#A_1_Introduction"> 1  Introduction </a>
 </li> <li> <a href="LibZFRelaxation.html#A_2_Isotropic_static_Gaussian_broadened_randomly_oriented_internal_fields"> 2  Isotropic static Gaussian broadened randomly oriented internal fields </a>
@@ -126,8 +133,8 @@ pre {
 </li> <li> <a href="LibZFRelaxation.html#A_4_Static_Gaussian_distributed_fields_with_uniaxial_anisotropy"> 4  Static Gaussian distributed fields with uniaxial anisotropy </a>
 </li></ul> 
 </div>
-<a name="IntroDuction"></a>
-<h1><a name="A_1_Introduction"></a> 1  Introduction </h1>
+<span id="IntroDuction"></span>
+<h1 id="A_1_Introduction"> 1  Introduction </h1>
 <p></p>
 <code>libZFRelaxation</code> is a collection of <code>C++</code> classes using the <code><a href="MusrFit.html">musrfit</a></code> <code><a href="MusrFit.html#UserFunctions1">user-function interface</a></code> in order to facilitate the usage in conjunction with <code>musrfit</code>. The classes contained in this library implement the calculation of some additional zero-field &mu;SR relaxation functions which are not built-in into <code>musrfit</code>.
 <p></p>
@@ -136,9 +143,9 @@ In the following the use of the implemented functions is shortly introduced&mdas
 If these classes prove useful and results obtained through them are part of scientific publications,
 an acknowledgement of the use of the library is appreciated.
 <p></p>
-<h1><a name="A_2_Isotropic_static_Gaussian_broadened_randomly_oriented_internal_fields"></a> 2  Isotropic static Gaussian broadened randomly oriented internal fields </h1>
+<h1 id="A_2_Isotropic_static_Gaussian_broadened_randomly_oriented_internal_fields"> 2  Isotropic static Gaussian broadened randomly oriented internal fields </h1>
 <p></p>
-E. I. Kornilov and V. Yu. Pomjakushin, Phys. Lett. A <b>153</b>, 364&#150;367 (1991), doi: <a href="http://dx.doi.org/10.1016/0375-9601(91)90959-C" target="_top">10.1016/0375-9601(91)90959-C</a>
+E. I. Kornilov and V. Yu. Pomjakushin, Phys. Lett. A <b>153</b>, 364&#150;367 (1991), doi: <a href="http://dx.doi.org/10.1016/0375-9601(91)90959-C">10.1016/0375-9601(91)90959-C</a>
 <p></p>
 <p style="text-align:center">
 <img alt="\mathcal{P}(t) &#61; \left(1-\alpha\right)\exp\left(-\frac{\sigma&#95;{\mathrm{L}}^2t^2}{2}\right)+\alpha\left(\cos\left(2\pi\nu t\right)-\frac{\sigma&#95;{\mathrm{T}}^2t}{2\pi\nu}\sin\left(2\pi\nu t\right)\right)\exp\left(-\frac{\sigma&#95;{\mathrm{T}}^2t^2}{2}\right)" class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_fca91646b118061038b53ada5563c17c.png" title="ZFMagGss" />
@@ -154,9 +161,9 @@ The parameters are: <ol>
 </li> <li> the "longitudinal depolarization rate" &sigma;<sub>L</sub> (&mu;s<sup>-1</sup>) (= 0 in the article).
 </li></ol> 
 <p></p>
-<h1><a name="A_3_Isotropic_static_Lorentzian_broadened_randomly_oriented_internal_fields"></a> 3  Isotropic static Lorentzian broadened randomly oriented internal fields </h1>
+<h1 id="A_3_Isotropic_static_Lorentzian_broadened_randomly_oriented_internal_fields"> 3  Isotropic static Lorentzian broadened randomly oriented internal fields </h1>
 <p></p>
-M. I. Larkin, Y. Fudamoto, I. M. Gat, A. Kinkhabwala, K. M. Kojima, G. M. Luke, J. Merrin, B. Nachumi, Y. J. Uemura, M. Azuma, T. Saito, and M. Takano, Physica B <b>289&#150;290</b>, 153&#150;156 (2000), doi: <a href="http://dx.doi.org/10.1016/S0921-4526(00)00337-9"" target="_top">10.1016/S0921-4526(00)00337-9</a>
+M. I. Larkin, Y. Fudamoto, I. M. Gat, A. Kinkhabwala, K. M. Kojima, G. M. Luke, J. Merrin, B. Nachumi, Y. J. Uemura, M. Azuma, T. Saito, and M. Takano, Physica B <b>289&#150;290</b>, 153&#150;156 (2000), doi: <a href="http://dx.doi.org/10.1016/S0921-4526(00)00337-9"">10.1016/S0921-4526(00)00337-9</a>
 <p></p>
 <p style="text-align:center">
 <img alt="\mathcal{P}(t) &#61; \left(1-\alpha\right)\exp\left(-a&#95;{\mathrm{L}}t\right) + \alpha\left(\cos\left(2\pi\nu t\right)-\frac{a&#95;{\mathrm{T}}}{2\pi\nu}\sin\left(2\pi\nu t\right)\right)\exp\left(-a&#95;{\mathrm{T}}t\right)" class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_975f948b57199037b2b8bfb5e986b6a9.png" title="ZFMagExp" />
@@ -172,9 +179,9 @@ The parameters are: <ol>
 </li> <li> the "longitudinal depolarization rate" a<sub>L</sub> (&mu;s<sup>-1</sup>) (= 0 in the article).
 </li></ol> 
 <p></p>
-<h1><a name="A_4_Static_Gaussian_distributed_fields_with_uniaxial_anisotropy"></a> 4  Static Gaussian distributed fields with uniaxial anisotropy </h1>
+<h1 id="A_4_Static_Gaussian_distributed_fields_with_uniaxial_anisotropy"> 4  Static Gaussian distributed fields with uniaxial anisotropy </h1>
 <p></p>
-G. Solt, Hyperfine Interactions <b>96</b>, 167&#150;175 (1995), doi: <a href="http://dx.doi.org/10.1007/BF02066280" target="_top">10.1007/BF02066280</a>
+G. Solt, Hyperfine Interactions <b>96</b>, 167&#150;175 (1995), doi: <a href="http://dx.doi.org/10.1007/BF02066280">10.1007/BF02066280</a>
 <p></p>
 <p style="text-align:center">
 <img alt="\mathcal{P}(t) &#61; \frac{1}{2}\sin^2\Theta + \left(\frac{3}{2}\cos^2\Theta-\frac{1}{2}\right)f&#95;1\left(\epsilon\right) + \sin^2\Theta f&#95;2(\epsilon, \sigma&#95;1, t) + \left(\frac{3}{2}\cos^2\Theta-\frac{1}{2}\right)f&#95;3\left(\epsilon, \sigma&#95;1, t\right)," class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_4611c56f1556464dd8a6eaabbe070c05.png" title="UniaxialStatGssKT" />
@@ -203,83 +210,29 @@ The parameters are: <ol>
 </li> <li> &Theta; (&deg;).
 </li></ol> 
 <p></p>
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+<h1 id="A_61_61msr2data_61_61">  <code><b>msr2data</b></code> </h1>
 <p></p>
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-      	
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-<h1><a name="A_61_61msr2data_61_61"></a>  <code><b>msr2data</b></code> </h1>
-<p></p>
-<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
+<div class="foswikiToc" id="foswikiTOC"> <ul>
 <li> <a href="Msr2Data.html#A_61_61msr2data_61_61"> msr2data </a>
 </li> <li> <a href="Msr2Data.html#A_1_Introduction"> 1  Introduction </a>
 </li> <li> <a href="Msr2Data.html#A_2_Basic_Types_of_Usage"> 2  Basic Types of Usage </a>
@@ -134,70 +176,72 @@ pre {
 </li></ul> 
 </div>
 <p></p>
-<a name="IntroDuction"></a>
-<h1><a name="A_1_Introduction"></a> 1  Introduction </h1>
-<code>msr2data</code> (originally written by B. M. Wojek) is a program implemented in <code>C++</code>. Its purpose is to process multiple <code><a href="MusrFit.html">musrfit</a></code> msr files with the same parameters and summarize the fitting results either in a TRIUMF <strong>DB</strong> <a name="FootNote1text"></a><span class='FootNoteTextLink' title=' For an abridged description of this format see <a href="http://musr.org/xyfit/dbformat.html" target="_top">here</a>. The <strong>DB</strong> files produced by <code>msr2data</code> can be viewed for instance with <a href="http://musr.org/muview/" target="_top">&mu;View</a>, however, they are <em>not completely</em> backward-compatible to the original "db language" since the parameter names can be longer than five or six characters! In order to establish this backward compatibility (if needed) the user has to ensure the correct length of the parameter names in the msr files!'><a href="#FootNote1note" class="foswikiCurrentTopicLink">(1)</a></span> or a <strong>column ASCII</strong> file. It evolved from a script called <code>mlog2db</code> which has been written only for collecting fit results of <a href="http://lmu.web.psi.ch/lem/" target="_top">LEM</a> data stored in mlog files generated by <code>musrfit</code> and putting them together in a file with the <strong>DB</strong> format for further analysis. Therefore, any peculiarities, e.g. in supplying options to <code>msr2data</code> are owed its original purpose.
-<code>msr2data</code> is <a href="http://www.gnu.org/philosophy/free-sw.html" target="_top">free software</a> and licensed under the <a href="http://www.gnu.org/licenses/old-licenses/gpl-2.0.html" target="_top">GNU GPL version 2</a> or any later version (at your option).
+<span id="IntroDuction"></span>
+<h1 id="A_1_Introduction"> 1  Introduction </h1>
+<code>msr2data</code> (originally written by B. M. Wojek) is a program implemented in <code>C++</code>. Its purpose is to process multiple <code><a href="MusrFit.html">musrfit</a></code> msr files with the same parameters and summarize the fitting results either in a TRIUMF <strong>DB</strong> <a name="FootNote1text"></a><span class="FootNoteTextLink" title=" For an abridged description of this format see &#91;&#91;http&#58;&#47;&#47;musr&#46;org&#47;xyfit&#47;dbformat&#46;html&#93;&#91;here&#93;&#93;&#46; The &#42;DB&#42; files produced by &#61;msr2data&#61; can be viewed for instance with &#91;&#91;http&#58;&#47;&#47;musr&#46;org&#47;muview&#47;&#93;&#91;&#38;mu&#59;View&#93;&#93;&#44; however&#44; they are <em>not completely</em> backward&#45;compatible to the original &#34;db language&#34; since the parameter names can be longer than five or six characters&#33; In order to establish this backward compatibility &#40;if needed&#41; the user has to ensure the correct length of the parameter names in the msr files&#33;"><a class="foswikiCurrentTopicLink" href="#FootNote1note">(1)</a></span> or a <strong>column ASCII</strong> file. It evolved from a script called <code>mlog2db</code> which has been written only for collecting fit results of <a href="http://lmu.web.psi.ch/lem/">LEM</a> data stored in mlog files generated by <code>musrfit</code> and putting them together in a file with the <strong>DB</strong> format for further analysis. Therefore, any peculiarities, e.g. in supplying options to <code>msr2data</code> are owed its original purpose.
+<code>msr2data</code> is <a href="http://www.gnu.org/philosophy/free-sw.html">free software</a> and licensed under the <a href="http://www.gnu.org/licenses/old-licenses/gpl-2.0.html">GNU GPL version 2</a> or any later version (at your option).
 <p></p>
 Before the usage of msr2data will be explained in greater detail first be aware of the following:
 <p></p>
-<strong><span class='foswikiRedFG'>If using msr2data always bear in mind <a href="#KnownLimitations" class="foswikiCurrentTopicLink">its limitations</a>!</span></strong>
+<strong><span class='foswikiRedFG'>If using msr2data always bear in mind <a class="foswikiCurrentTopicLink" href="#KnownLimitations">its limitations</a>!</span></strong>
 <p></p>
 <p></p>
 <p></p>
 Notes
 <p></p>
-<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="#FootNote1text" class="foswikiCurrentTopicLink"> <strong>1</strong> </a></span>: <span class="FootNote"> For an abridged description of this format see <a href="http://musr.org/xyfit/dbformat.html" target="_top">here</a>. The <strong>DB</strong> files produced by <code>msr2data</code> can be viewed for instance with <a href="http://musr.org/muview/" target="_top">&mu;View</a>, however, they are <em>not completely</em> backward-compatible to the original "db language" since the parameter names can be longer than five or six characters! In order to establish this backward compatibility (if needed) the user has to ensure the correct length of the parameter names in the msr files!</span> 
+<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="#FootNote1text"><b>1</b></a></span>: <span class="FootNote"> For an abridged description of this format see <a href="http://musr.org/xyfit/dbformat.html">here</a>. The <strong>DB</strong> files produced by <code>msr2data</code> can be viewed for instance with <a href="http://musr.org/muview/">&mu;View</a>, however, they are <em>not completely</em> backward-compatible to the original "db language" since the parameter names can be longer than five or six characters! In order to establish this backward compatibility (if needed) the user has to ensure the correct length of the parameter names in the msr files!</span> 
 <p></p>
 <p></p>
 <p></p>
 <hr />
 <p></p>
-<a name="BasicTypesOfUsage"></a>
-<h1><a name="A_2_Basic_Types_of_Usage"></a> 2  Basic Types of Usage </h1>
-Apart from numerous <a href="#OptionalParameters" class="foswikiCurrentTopicLink">optional parameters</a> that might be set or not, in principle there are four different ways of calling <code>msr2data</code>. These differ in how the list of runs which should be processed is supplied: <dl>
+<span id="BasicTypesOfUsage"></span>
+<h1 id="A_2_Basic_Types_of_Usage"> 2  Basic Types of Usage </h1>
+Apart from numerous <a class="foswikiCurrentTopicLink" href="#OptionalParameters">optional parameters</a> that might be set or not, in principle there are four different ways of calling <code>msr2data</code>. These differ in how the list of runs which should be processed is supplied: <dl>
 <dt> msr2data &lt;run&gt; &lt;extension&gt; [optional parameters] </dt><dd> A single run number.
 </dd> <dt> msr2data &lt;firstRunNo&gt; &lt;lastRunNo&gt; &lt;extension&gt; [optional parameters] </dt><dd> An interval of run numbers is specified through the first and the last run number. The condition <strong>&lt;firstRunNo&gt;  &lt; &lt;lastRunNo&gt;</strong> is <em>not</em> necessary.
-</dd> <dt> msr2data \[&lt;run1&gt; &lt;run2&gt; ... &lt;runN&gt; \] &lt;extension&gt; [optional parameters] </dt><dd> A space separated list of run numbers can be enclosed in <strong>[</strong> and <strong>]</strong>. Every run that should be processed has to be specified explicitly by its run number.
-</dd> <dt> msr2data &lt;runListFileName&gt; &lt;extension&gt; [optional parameters] </dt><dd> An ASCII file containing a list of run numbers and optional external parameters is passed to <code>msr2data</code>. For the structure of the ASCII file see <a href="#RunListStructure" class="foswikiCurrentTopicLink">below</a>.
+</dd> <dt> msr2data \[ &lt;runList&gt; \] &lt;extension&gt; [optional parameters] </dt><dd> Where &lt;runList&gt; is one or a combination of the following:(i) <strong>&lt;run0&gt;, &lt;run1&gt;, &lt;run2&gt;, ... &lt;runN&gt;</strong> : run numbers, e.g. 123 124, (ii)  <strong>&lt;run0&gt;-&lt;runN&gt;</strong> : a range, e.g. 123-125 -&gt; 123 124 125, (iii) <strong>&lt;run0&gt;:&lt;runN&gt;:&lt;step&gt;</strong> : a sequence, e.g. 123:127:2 -&gt; 123 125 127. &lt;step&gt; has to be a <strong>positive</strong> integer. A &lt;runList&gt; can also combine (i)-(iii), e.g. 123 128-130 133, etc.    
+</dd> <dt> msr2data &lt;runListFileName&gt; &lt;extension&gt; [optional parameters] </dt><dd> An ASCII file containing a list of run numbers and optional external parameters is passed to <code>msr2data</code>. For the structure of the ASCII file see <a class="foswikiCurrentTopicLink" href="#RunListStructure">below</a>.
 </dd></dl> 
 <p></p>
 All four basic types of calling <code>msr2data</code> contain the <em>mandatory</em> file-name <strong>&lt;extension&gt;</strong> passed right after the list of runs. The meaning of this <strong>&lt;extension&gt;</strong> should become clear after giving examples for all four cases:
-<pre class="bash">msr2data 8472 &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a href="#OptionalParameters" class="foswikiCurrentTopicLink">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code>.
-<pre class="bash">msr2data 8472 8474 &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a href="#OptionalParameters" class="foswikiCurrentTopicLink">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code>, <code><b>8473_tf_h13.msr</b></code>, and <code><b>8474_tf_h13.msr</b></code>.
-<pre class="bash">msr2data &#91;8472 8470] &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a href="#OptionalParameters" class="foswikiCurrentTopicLink">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code> and <code><b>8470_tf_h13.msr</b></code>.
-<pre class="bash">msr2data run.list &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a href="#OptionalParameters" class="foswikiCurrentTopicLink">the -o option</a>) from all runs listed in the ASCII file <code><b>run.list</b></code> in the working directory. In this file it is also possible to include external parameters which should be put in the resulting <strong>DB</strong> file. The structure of the <code><b>run.list</b></code> is the following:
-<a name="RunListStructure"></a>
+<pre class="bash">msr2data 8472 &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a class="foswikiCurrentTopicLink" href="#OptionalParameters">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code>.
+<pre class="bash">msr2data 8472 8474 &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a class="foswikiCurrentTopicLink" href="#OptionalParameters">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code>, <code><b>8473_tf_h13.msr</b></code>, and <code><b>8474_tf_h13.msr</b></code>.
+<pre class="bash">msr2data &#91;8472 8470&#93; &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a class="foswikiCurrentTopicLink" href="#OptionalParameters">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code> and <code><b>8470_tf_h13.msr</b></code>.
+<pre class="bash">msr2data &#91;8470:8474:2&#93; &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a class="foswikiCurrentTopicLink" href="#OptionalParameters">the -o option</a>) from <code><b>8470_tf_h13.msr</b></code>, <code><b>8472_tf_h13.msr</b></code>, and <code><b>8474_tf_h13.msr</b></code>.
+<pre class="bash">msr2data run.list &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a class="foswikiCurrentTopicLink" href="#OptionalParameters">the -o option</a>) from all runs listed in the ASCII file <code><b>run.list</b></code> in the working directory. In this file it is also possible to include external parameters which should be put in the resulting <strong>DB</strong> file. The structure of the <code><b>run.list</b></code> is the following:
+<span id="RunListStructure"></span>
 <pre>
 RUN VAR1 VAR2 VAR3 ...
 8460 200 27.1 46.2 ...
 8472 205 27.1 46.3 ...
 8453 210 27.2 45.9 ...
-<EFBFBD>     <EFBFBD>    <EFBFBD>    <EFBFBD>
-<EFBFBD>     <EFBFBD>    <EFBFBD>    <EFBFBD>
-<EFBFBD>     <EFBFBD>    <EFBFBD>    <EFBFBD>
+·     ·    ·    ·
+·     ·    ·    ·
+·     ·    ·    ·
 </pre>
 <span class='foswikiRedFG'>The first not commented and not empty line determines the parameter names and labels and has to be present!</span><br/>
 It is allowed to add comments (with a preceding <strong>#</strong>) or empty lines to the run-list file. 
 <p></p>
 The following should be mentioned together with the above examples: <ul>
 <li> The output files in the examples above are only newly created if they did not exist before invoking <strong>msr2data</strong>. If the files were already present the msr-file data would be appended!
-</li> <li> If the files have been newly created, also the <strong>DB</strong> file header is written. If the files were present before, only the data blocks are appended. The output of the header can either be forced or completely suppressed with the <a href="#OptionalParameters" class="foswikiCurrentTopicLink">header and noheader options</a> as shall be seen later.
+</li> <li> If the files have been newly created, also the <strong>DB</strong> file header is written. If the files were present before, only the data blocks are appended. The output of the header can either be forced or completely suppressed with the <a class="foswikiCurrentTopicLink" href="#OptionalParameters">header and noheader options</a> as shall be seen later.
 </li></ul> 
-<a name="NoExtension"></a> <ul>
+<span id="NoExtension"></span> <ul>
 <li> <span class='foswikiRedFG'>If the <code>musrfit</code> output files do not have an &lt;extension&gt; as specified above like <code><b>8472.msr</b></code> one has to call <code>msr2data</code> like in the following example:</span> <pre class="bash">
 msr2data 8472 8460 &#34;&#34;
 </pre>
 </li></ul> 
 <p></p>
-<a name="OptionalParameters"></a>
-<h1><a name="A_3_Optional_Parameters"></a> 3  Optional Parameters </h1>
+<span id="OptionalParameters"></span>
+<h1 id="A_3_Optional_Parameters"> 3  Optional Parameters </h1>
 As mentioned already above there are some optional parameters which change the behavior of <code>msr2data</code> and can be passed in any order. Here is a complete list: <dl>
 <dt> data </dt><dd> The output file format is changed to a simple column ASCII file (default output file name: <code><b>out.dat</b></code>).
 </dd> <dt> new </dt><dd> An existing output file is deleted before new information is written to it.
 </dd> <dt> header </dt><dd> Force the output of the file header&#151;even if the output file was present before.
 </dd> <dt> noheader </dt><dd> The output of the file header is suppressed&#151;also if the output file is newly created.<br>If either both or none of the header options are given, <code>msr2data</code> writes the file header only to new files and it solely appends the data blocks to an existing output file assuming that the header is present already.
 </dd> <dt> nosummary </dt><dd> There will be no attempt to read additional information like the temperature or the applied magnetic field from the data files even if these information were present there.
+</dd> <dt> paramList &lt;param&gt; </dt><dd> option used to select the parameters which shall be exported. &lt;param&gt; is a list of parameter numbers to be exported. Allowed lists are: &lt;startNo&gt;-&lt;endNo&gt;, e.g. 1-16 will export parameters 1 to 16. Space separated numbers, e.g.: 1 3 5. A combination of both is possible, e.g. 1-16 19 31 62, and so on. 
 </dd> <dt> -o&lt;outputFileName&gt;, -o &lt;outputFileName&gt; </dt><dd> The processed data will be written to the file <strong>&lt;outputFileName&gt;</strong> instead of the default <code><b>out.db</b></code> or <code><b>out.dat</b></code>. If <strong>&lt;outputFileName&gt;</strong> is equal to <strong>none</strong> (case-insensitive) the parameter data are <em>not appended</em> to any output file.
 </dd> <dt> fit </dt><dd> Additionally to the final data collection <code>msr2data</code> will invoke musrfit to fit the specified runs. All msr files are assumed to be present, none is newly generated!
 </dd> <dt> fit-&lt;template&gt;[!] </dt><dd> Additionally to the final data collection <code>msr2data</code> will generate msr files for the runs specified in the list of runs and invoke <code>musrfit</code> for performing fits of the data. As template for the first run the file <code><b>&lt;template&gt;&lt;extension&gt;.msr</b></code> (or if not available: <code><b>&lt;template&gt;&lt;extension&gt;.mlog</b></code>) is used; the subsequent input files will be created using the msr output of the last processed runs ("chain fit"). However, if for <em>all</em> runs only the given template should be used one has to append an exclamation mark (<strong>!</strong>) to the <strong>&lt;template&gt;</strong>.
@@ -212,9 +256,9 @@ msr2data 8400 8460 &#95;tf&#95;h13 -oABC.db fit-8472
 </pre>
 Using <code><b>8472_tf_h13.msr</b></code> as first template, <code>msr2data</code> generates subsequent msr input files <code><b>8400_tf_h13.msr</b></code> through <code><b>8460_tf_h13.msr</b></code>, calls <code>musrfit</code> to perform a fit of these files and collects the results of the fits together with the <strong>DB</strong> header in the new file <code><b>ABC.db</b></code>. Additionally, some information about external parameters like the temperature will be passed to <code><b>ABC.db</b></code> if it is present in the data files.
 <pre class="bash">
-msr2data &#91;8500 8505] &#95;zf fit-8472 noheader nosummary -o DEF.db 
+msr2data &#91;8500 8502-8504 8507&#93; &#95;zf fit-8472 noheader nosummary -o DEF.db 
 </pre>
-Using <code><b>8472_zf.msr</b></code> as first template, <code>msr2data</code> generates subsequent msr input files <code><b>8500_zf.msr</b></code> and <code><b>8505_zf.msr</b></code>, calls <code>musrfit</code> to perform a fit of these files and collects the results of the fits in the file <code><b>DEF.db</b></code> without writing the <strong>DB</strong> file header or attempting to read additional information from the data files.
+Using <code><b>8472_zf.msr</b></code> as first template, <code>msr2data</code> generates subsequent msr input files <code><b>8500_zf.msr</b></code>, <code><b>8502_zf.msr</b></code>, <code><b>8503_zf.msr</b></code>, <code><b>8504_zf.msr</b></code> and <code><b>8507_zf.msr</b></code>, calls <code>musrfit</code> to perform a fit of these files and collects the results of the fits in the file <code><b>DEF.db</b></code> without writing the <strong>DB</strong> file header or attempting to read additional information from the data files.
 <pre class="bash">
 msr2data 8595 8585 &#34;&#34; noheader fit-8472! -oGHI.dat data nosummary -k 
 </pre>
@@ -227,13 +271,19 @@ Take the <strong>given</strong> msr files <code><b>8472.msr</b></code> through <
 msr2data 8472 8475 &#95;tf&#95;h13 msr-8471!
 </pre>
 Using <code><b>8471_tf_h13.msr</b></code> as template for <em>all</em> runs, <code>msr2data</code> generates the msr input files <code><b>8472_tf_h13.msr</b></code> through <code><b>8475_tf_h13.msr</b></code>. <span class='foswikiRedFG'>No fitting will be performed and no DB or ASCII output will be generated!</span>
+<pre class="bash">
+msr2data &#91;8472 8475-8479&#93; &#95;tf&#95;h13 paramList 1-16 data -o bestData.dat
+</pre>
+Will collect the parameters 1 to 16 from the msr-files <code><b>8472_tf_h13.msr</b></code>, <code><b>8475_tf_h13.msr</b></code>, <code><b>8476_tf_h13.msr</b></code>, <code><b>8477_tf_h13.msr</b></code>, <code><b>8478_tf_h13.msr</b></code>, and <code><b>8479_tf_h13.msr</b></code> and write these parameters into a column like output file <code><b>bestData.dat</b></code>.
 <p></p>
-<a name="TheGlobalMode"></a>
-<h1><a name="A_4_The_Global_Mode"></a> 4  The Global Mode </h1>
-Apart from all the options described <a href="#OptionalParameters" class="foswikiCurrentTopicLink">above</a> there is another program option: <strong>global</strong>. This option changes the general behavior of <code>msr2data</code> in that way that instead of processing one msr file for each run it combines all specified runs in one single msr file with the possibility to define common parameters for all runs as well as run-specific parameters. When writing the obtained parameters to a DB file or a column-structured ASCII file that single msr file is read and the parameters valid for each run are extracted. The <strong>global</strong> option can be used in conjunction with any of the described <a href="#BasicTypesOfUsage" class="foswikiCurrentTopicLink">invocations</a> of <code>msr2data</code> and together with all options stated <a href="#OptionalParameters" class="foswikiCurrentTopicLink">above</a>.
 <p></p>
-<a name="GlobalFileGeneration"></a>
-<h2><a name="A_4.1_File_Generation"></a> 4.1  File Generation </h2>
+<p></p>
+<span id="TheGlobalMode"></span>
+<h1 id="A_4_The_Global_Mode"> 4  The Global Mode </h1>
+Apart from all the options described <a class="foswikiCurrentTopicLink" href="#OptionalParameters">above</a> there is another program option: <strong>global</strong>. This option changes the general behavior of <code>msr2data</code> in that way that instead of processing one msr file for each run it combines all specified runs in one single msr file with the possibility to define common parameters for all runs as well as run-specific parameters. When writing the obtained parameters to a DB file or a column-structured ASCII file that single msr file is read and the parameters valid for each run are extracted. The <strong>global</strong> option can be used in conjunction with any of the described <a class="foswikiCurrentTopicLink" href="#BasicTypesOfUsage">invocations</a> of <code>msr2data</code> and together with all options stated <a class="foswikiCurrentTopicLink" href="#OptionalParameters">above</a>.
+<p></p>
+<span id="GlobalFileGeneration"></span>
+<h2 id="A_4.1_File_Generation"> 4.1  File Generation </h2>
 The general idea of this mode is to generate a global msr file on the basis of a working single-run msr file. For this purpose a single-run template containing information about common and run-specific parameters should be created. These parameters are identified through their parameter names: <dl>
 <dt> run-specific parameters </dt><dd> these parameters are tagged with the current run number in the format <strong>%0Xu</strong>, i.e. <strong>X</strong> digits with leading zeros, at the end of the parameter name, e.g. for a 4-digit-formatted run number <strong>alpha0123</strong> if the run number was <strong>123</strong> or for a 8-digit-formatted run number <strong>alpha00123456</strong> if the run number was <strong>123456</strong>. <strong>X</strong> has to be at least 4.
 </dd> <dt> common parameters </dt><dd> all parameters that are not run specific
@@ -278,32 +328,32 @@ During this reorganization all the affected parameter occurrences are changed ac
 <p></p>
 <span class='foswikiRedFG'>Please be aware of the fact that comments in the template msr file are <em>not</em> propagated to the newly generated global msr file!</span>
 <p></p>
-<h2><a name="A_4.2_Parameter_Extraction"></a> 4.2  Parameter Extraction </h2>
-After fitting some model to the specified data the fit parameters can be extracted from the global msr file to a <strong>DB</strong> or column-structured ASCII file&mdash;as usual this includes also parameters stored in the run data files or externally specified parameters given in a <a href="#RunListStructure" class="foswikiCurrentTopicLink">run-list file</a>.
+<h2 id="A_4.2_Parameter_Extraction"> 4.2  Parameter Extraction </h2>
+After fitting some model to the specified data the fit parameters can be extracted from the global msr file to a <strong>DB</strong> or column-structured ASCII file&mdash;as usual this includes also parameters stored in the run data files or externally specified parameters given in a <a class="foswikiCurrentTopicLink" href="#RunListStructure">run-list file</a>.
 In order to reach this goal the global msr file has to obey certain rules: <ul>
-<li> The order of the parameters has to match the one described <a href="#GlobalFileGeneration" class="foswikiCurrentTopicLink">above</a>, meaning the common parameters are listed first followed by the same number of parameters specific to each run tagged by the according run numbers at the end of the parameter names and having the same order as the specified list of runs.
+<li> The order of the parameters has to match the one described <a class="foswikiCurrentTopicLink" href="#GlobalFileGeneration">above</a>, meaning the common parameters are listed first followed by the same number of parameters specific to each run tagged by the according run numbers at the end of the parameter names and having the same order as the specified list of runs.
 </li> <li> The RUN blocks have to be ordered according to the list of runs to be processed.
 </li></ul> 
-Following these rules&mdash;which is achieved most easily by generating the global msr file using <code>msr2data</code> as shown <a href="#GlobalFileGeneration" class="foswikiCurrentTopicLink">above</a>&mdash;the parameters can be extracted e.g. like <pre class="bash">
+Following these rules&mdash;which is achieved most easily by generating the global msr file using <code>msr2data</code> as shown <a class="foswikiCurrentTopicLink" href="#GlobalFileGeneration">above</a>&mdash;the parameters can be extracted e.g. like <pre class="bash">
 msr2data 8471 8470 &#95;example global data -o globalFit.dat
 </pre>
 This will read in the file <code><b>8471+global_example.msr</b></code>, extract for each run all relevant parameters from the msr file as well as from the according data files (if available) and append all of them in columns to the ASCII file <code><b>globalFit.dat</b></code>.
 <p></p>
-<a name="GlobalPlus"></a>
-<h2><a name="A_4.3_The_Extended_Global_Mode"></a> 4.3  The Extended Global Mode </h2>
+<span id="GlobalPlus"></span>
+<h2 id="A_4.3_The_Extended_Global_Mode"> 4.3  The Extended Global Mode </h2>
 If a new global input file is generated, it is also possible to do an automatic pre-analysis for each single run using the specified template first; afterwards the run-specific parameters of these single-run msr files are collected in the global msr file. In special cases this might be useful to obtain a better set of starting values for the parameters, however, in most cases it will not replace the "manual review" of the generated global input file. The option is activated by choosing the keyword <strong>global+</strong>. For example <pre class="bash">
 msr2data 8471 8470 &#95;example global+ msr-8472
 </pre>
 Here, <code><b>8472_example.msr</b></code> is first used as template to generate the file <code><b>8471-OneRunFit_example.msr</b></code>, then <code>musrfit</code> is called for it, the result is used to generate <code><b>8470-OneRunFit_example.msr</b></code> and <code>musrfit</code> is called for that file. Finally, the global fit file <code><b>8471+global_example.msr</b></code> is produced&mdash;including the fit results of the OneRunFit files for the run-specific parameters.<br>
-By appending an exclamation mark <strong>!</strong> to the <strong>global+</strong> option, the given template will be used for every new file generation (similar to the <strong>fit</strong> option explained <a href="#OptionalParameters" class="foswikiCurrentTopicLink">before</a>). The <strong>+[!]</strong> extension will be ignored, if no new global input file is generated.<br>
+By appending an exclamation mark <strong>!</strong> to the <strong>global+</strong> option, the given template will be used for every new file generation (similar to the <strong>fit</strong> option explained <a class="foswikiCurrentTopicLink" href="#OptionalParameters">before</a>). The <strong>+[!]</strong> extension will be ignored, if no new global input file is generated.<br>
 The single run msr files are not deleted at the moment. The information contained in them might be useful for some people. Of course the data can also be collected by <code>msr2data</code>. E.g. in order to produce a <strong>DB</strong> file <code><b>OneRunFits.db</b></code> one could call <pre class="bash">
 msr2data 8471 8470 -OneRunFit&#95;example -o OneRunFits.db
 </pre>
 <p></p>
 <span class='foswikiRedFG'>Please be aware that the program in this mode always generates new single-run msr files and always calls <code>musrfit</code> for them. In case there are already single-run fits present, these cannot be used in conjunction with this option. The program on purpose behaves in this way in order to ensure the file integrity and correct parameter order within these files.</span>
 <p></p>
-<a name="KnownLimitations"></a>
-<h1><a name="A_5_Known_Limitations"></a> 5  Known Limitations </h1> <ul>
+<span id="KnownLimitations"></span>
+<h1 id="A_5_Known_Limitations"> 5  Known Limitations </h1> <ul>
 <li> The indexing run number of the msr file has to be at the begin of every filename.
 </li> <li> Within the data file name the <strong>RUN#</strong> has the format <strong>%0Xu</strong>, i.e. <strong>X</strong> digits with leading zeros, and has to be the rightmost number given in this format in the file name. <strong>X</strong> has to be at least 4. The highest treatable run number is 2<sup>32</sup>-1 = 4294967295.
 </li> <li> In order to keep <code>msr2data</code> working properly the msr files should only contain <em><span class='foswikiRedFG'>one</span> STATISTIC block at the end of the file</em> and <i><span class='foswikiRedFG'>one</span> FITPARAMETER block right after the TITLE</i>&mdash;<code>musrfit</code> itself allows to have more creative msr files...
@@ -311,12 +361,12 @@ msr2data 8471 8470 -OneRunFit&#95;example -o OneRunFits.db
 </li> <li> <code>msr2data</code> will write only up to <em>two successive</em> empty lines in newly generated msr files. In case more subsequent empty lines are encountered in a template file, these are <em>not</em> copied! Actually, this measure is not a limitation but has been introduced to keep the msr files in a reasonable shape.
 </li></ul> 
 <p></p>
-<a name="MusrGuiInterface"></a>
-<h1><a name="A_6_The_Graphical_User_Interface_Provided_by_61_61musrgui_61_61_47_61_61musredit_61_61"></a> 6  The Graphical User Interface Provided by <code><b>musrgui</b></code> / <code><b>musredit</b></code> </h1>
+<span id="MusrGuiInterface"></span>
+<h1 id="A_6_The_Graphical_User_Interface_Provided_by_61_61musrgui_61_61_47_61_61musredit_61_61"> 6  The Graphical User Interface Provided by <code><b>musrgui</b></code> / <code><b>musredit</b></code> </h1>
 <code><a href="MusrGui.html">musrgui/musredit</a></code>, editors designed especially for the manipulation of <code>musrfit</code> msr files and graphical front ends to <code><a href="MusrFit.html">musrfit</a></code>, offer an almost self-explanatory graphical user interface to <code>msr2data</code> depicted below:<br>
-<img src="../pub/MUSR/Msr2Data/msr2data-input-tabs.png" alt="msr2data-input-tabs.png" width='612' height='605' align="right" /> <dl>
-<dt> <span class='foswikiRedFG'>1&ndash;3</span> </dt><dd> Choose one of the <a href="#BasicTypesOfUsage" class="foswikiCurrentTopicLink">ways</a> to specify your list of runs.
-</dd> <dt> <span class='foswikiRedFG'>4</span> </dt><dd> Give the file extension here, e.g. <strong>_zf</strong> for files like <code><b>8472_zf.msr</b></code>. If the files do not have an extension this field stays empty. <code>musrgui</code> / <code>musredit</code> take care of passing the <strong>""</strong> to <code>msr2data</code> as mentioned <a href="#NoExtension" class="foswikiCurrentTopicLink">above</a>.
+<img class='imagePlain imagePlain_right ' src='../pub/MUSR/Msr2Data/igp_589e1dc22ab7bf8fd9d5889da6e407f1_msr2data-input-tabs.png' alt='msr2data-input-tabs.png' title='msr2data-input-tabs.png' width='612' height='605'   style='' /> <dl>
+<dt> <span class='foswikiRedFG'>1&ndash;3</span> </dt><dd> Choose one of the <a class="foswikiCurrentTopicLink" href="#BasicTypesOfUsage">ways</a> to specify your list of runs.
+</dd> <dt> <span class='foswikiRedFG'>4</span> </dt><dd> Give the file extension here, e.g. <strong>_zf</strong> for files like <code><b>8472_zf.msr</b></code>. If the files do not have an extension this field stays empty. <code>musrgui</code> / <code>musredit</code> take care of passing the <strong>""</strong> to <code>msr2data</code> as mentioned <a class="foswikiCurrentTopicLink" href="#NoExtension">above</a>.
 </dd> <dt> <span class='foswikiRedFG'>5</span> </dt><dd> Activates the <strong>fit-&lt;template&gt;</strong> option if <strong>&lt;template&gt;</strong> is entered. In case the option "Chain Fit" is <em>not</em> set the given template will be used for the input-file generation for <em>all</em> runs to be fitted&mdash;otherwise the output of the first fit serves as template for the second and so on. The template field stays empty if no fits should be performed!
 </dd> <dt> <span class='foswikiRedFG'>6</span> </dt><dd> Activates the <strong>-o&lt;outputFileName&gt;</strong> option if <strong>&lt;outputFileName&gt;</strong> is entered. If nothing is entered the default output file <code><b>out.db</b></code> or <code><b>out.dat</b></code> is used.
 </dd> <dt> <span class='foswikiRedFG'>7</span> </dt><dd> If <em>not</em> set, the <strong>noheader</strong> option is passed to <code>msr2data</code>.
@@ -328,104 +378,63 @@ msr2data 8471 8470 -OneRunFit&#95;example -o OneRunFits.db
 </dd> <dt> <span class='foswikiRedFG'>13</span> </dt><dd> If set, the <strong>-t</strong> option is passed to <code>msr2data</code>.
 </dd> <dt> <span class='foswikiRedFG'>14</span> </dt><dd> If set, <code>msr2data</code> is called with the option <strong>msr-&lt;template&gt;</strong> (instead of <strong>fit-&lt;template&gt;</strong>) and hence is only producing the msr input files without any fitting.
 </dd> <dt> <span class='foswikiRedFG'>15</span> </dt><dd> If set, <code>msr2data</code> is called with the option <strong>fit</strong>, i.e. no template will be used to generate new msr input files; only existing files are fed to <code>musrfit</code>.
-</dd> <dt> <span class='foswikiRedFG'>16</span> </dt><dd> If set, <code>msr2data</code> is operating in the <a href="#TheGlobalMode" class="foswikiCurrentTopicLink">global mode</a>.
-</dd> <dt> <span class='foswikiRedFG'>17</span> </dt><dd> If set, <code>msr2data</code> is operating in the <a href="#GlobalPlus" class="foswikiCurrentTopicLink">extended global mode</a>.
+</dd> <dt> <span class='foswikiRedFG'>16</span> </dt><dd> If set, <code>msr2data</code> is operating in the <a class="foswikiCurrentTopicLink" href="#TheGlobalMode">global mode</a>.
+</dd> <dt> <span class='foswikiRedFG'>17</span> </dt><dd> If set, <code>msr2data</code> is operating in the <a class="foswikiCurrentTopicLink" href="#GlobalPlus">extended global mode</a>.
 </dd></dl> 
 <p></p>
-<a name="BugTracking"></a>
-<h1><a name="A_7_Bugtracking"></a> 7  Bugtracking </h1>
+<span id="BugTracking"></span>
+<h1 id="A_7_Bugtracking"> 7  Bugtracking </h1>
 <p></p>
-For reporting bugs or requesting new features and improvements please use the <a href="https://tracker.intranet.psi.ch/jira/browse/MUSR" target="_top">PSI Tracker</a> or send an e-mail to A. Suter.
+For reporting bugs or requesting new features and improvements please use the <a href="https://bitbucket.org/muonspin/musrfit/issues?status=new&amp;status=open">Bitbucket Issues</a>, <a href="https://tracker.psi.ch/jira/browse/MUSR">PSI Tracker</a> or send an e-mail to A. Suter.
 <p></p>
--- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> &amp; <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a> </div>
-<div class="foswikiContentFooter"></div><!-- -->
-<!-- -->
-<!-- -->
-<!-- -->
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-<h2 class='jqTabLabel'>Attachments <span class='foswikiAttachmentsCount'>(1)</span></h2>
-<div class='jqTabContents' >
-  <div class='foswikiFormSteps foswikiAttachmentsProcess'><span class='jqAjaxLoader'>&nbsp;</span></div>
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-<a name="topic-actions"></a>
-  <div class="patternTopicActions foswikiFormStep">
-	 <span class="patternActionButtons"><span><a href='https://intranet.psi.ch/wiki/bin/edit/MUSR/Msr2Data?t=1418910334' rel='nofollow' title='Edit this topic text' accesskey='e'><span class='foswikiAccessKey'>E</span>dit</a></span><span class='foswikiSeparator'>&nbsp;|&nbsp;</span><span class="foswikiRequiresChangePermission"><a href='https://intranet.psi.ch/wiki/bin/attach/MUSR/Msr2Data' rel='nofollow' title='Attach an image or document to this topic' accesskey='a'><span class='foswikiAccessKey'>A</span>ttach</a></span><span class='foswikiSeparator'>&nbsp;|&nbsp;</span><span><a href='Msr2Datac99a.html?cover=print;cover=print' rel='nofollow' title='Printable version of this topic' accesskey='p'><span class='foswikiAccessKey'>P</span>rint version</a></span><span class='foswikiSeparator'>&nbsp;|&nbsp;</span><span><a href='https://intranet.psi.ch/print/php/pdf.php?url=MUSR/Msr2Data?cover=print' title='PDF version of this topic'>PDF</a></span><span class='foswikiSeparator'>&nbsp;|&nbsp;</span><span><span class="foswikiRequiresChangePermission"><a href='https://intranet.psi.ch/wiki/bin/oops/MUSR/Msr2Data?template=oopshistory' rel='nofollow' title='View total topic history' accesskey='h'><span class='foswikiAccessKey'>H</span>istory</a></span>: r38&nbsp;<a rel="nofollow" href="https://intranet.psi.ch/wiki/bin/compare/MUSR/Msr2Data?rev1=37;rev2=38">&lt;</a>&nbsp;<a rel="nofollow" href="https://intranet.psi.ch/MUSR/Msr2Data?rev=37">r37</a>&nbsp;<a rel="nofollow" href="https://intranet.psi.ch/wiki/bin/compare/MUSR/Msr2Data?rev1=36;rev2=37">&lt;</a>&nbsp;<a rel="nofollow" href="https://intranet.psi.ch/MUSR/Msr2Data?rev=36">r36</a>&nbsp;<a rel="nofollow" href="https://intranet.psi.ch/wiki/bin/compare/MUSR/Msr2Data?rev1=35;rev2=36">&lt;</a>&nbsp;<a rel="nofollow" href="https://intranet.psi.ch/MUSR/Msr2Data?rev=35">r35</a></span><span class='foswikiSeparator'>&nbsp;|&nbsp;</span><span><a href='https://intranet.psi.ch/MUSR/Msr2Data?template=backlinksweb' rel='nofollow' title='Search the MUSR Web for topics that link to here' accesskey='b'><span class='foswikiAccessKey'>B</span>acklinks</a></span><span class='foswikiSeparator'>&nbsp;|&nbsp;</span><span><a href='https://intranet.psi.ch/MUSR/Msr2Data?raw=on' rel='nofollow' title='View without formatting' accesskey='v'><span class='foswikiAccessKey'>V</span>iew wiki text</a></span><span class='foswikiSeparator'>&nbsp;|&nbsp;</span><span><a href='https://intranet.psi.ch/MUSR/Msr2Data?refresh=on' title='Refresh images and LaTeX charts'>Refresh</a></span><span class='foswikiSeparator'>&nbsp;|&nbsp;</span><span><a href='https://intranet.psi.ch/MUSR/Msr2Data?template=more&amp;maxrev=38&amp;currrev=38' rel='nofollow' title='Delete or rename this topic; set parent topic; view and compare revisions' accesskey='m'><span class='foswikiAccessKey'>M</span>ore topic actions</a></span></span>
-  </div>
-</div></div><div class="patternInfo"><span class="patternRevInfo">Topic revision: r38 - 20 Jul 2011, wojek</span></div>
-</div>
-</div><div id="patternSideBar"><div id="patternClearHeaderLeft"></div>
-<div id="patternSideBarContents">
-<div class="patternLeftBarPersonal">
-<ul><li class="patternLogIn"><a href="https://intranet.psi.ch/wiki/bin/logon/MUSR/Msr2Data">Log In</a> or <a href="https://intranet.psi.ch/System/UserRegistration">Register</a></li></ul>
-</div>
+-- <a href="http://www.fsf.org/register_form?referrer=8369">BMW</a> &amp; <a href="http://lmu.web.psi.ch/lem/group.html">AS</a></div>
 <p></p>
 <p></p>
-<b>PSI Webs</b> <ul>
-<li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/psi.png" width="16" height="16" alt="psi" /></span> <a href="https://intranet.psi.ch/Main/WebHome">Main</a>
-</li> <li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/psi.png" width="16" height="16" alt="psi" /></span> <a href="https://intranet.psi.ch/Main/WebList">weitere Webs</a>
-</li></ul> 
-<hr />
-<b>System Webs</b> <ul>
-<li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/foswiki.png" width="16" height="16" alt="foswiki" /></span> <a href="https://intranet.psi.ch/Sandbox/WebHome">Sandbox</a>
-</li> <li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/foswiki.png" width="16" height="16" alt="foswiki" /></span> <a href="https://intranet.psi.ch/System/WebHome">Documentation</a>
-</li></ul> 
-<hr /> <ul>
-<li> <a href="https://intranet.psi.ch/MUSR/WebCreateNewTopic?parent=Msr2Data" target="_top"><span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/newtopic.png" width="16" height="16" alt="newtopic" /></span> Create New Topic</a> 
-</li> <li> <a href="WebTopicList.html"> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/index.png" width="16" height="16" alt="index" /></span> Show All Topics</a> 
-</li> <li> <a href="WebSearch.html"> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/searchtopic.png" width="16" height="16" alt="searchtopic" /></span> Search in Topics</a> 
-</li> <li> <a href="WebChanges.html"> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/changes.png" width="16" height="16" alt="changes" /></span> Recent Changes</a>
-</li> <li> <a href="WebNotify.html"> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/notify.png" width="16" height="16" alt="notify" /></span> Define Notifications</a>
-</li></ul> 
-<p></p>
-</div></div>
-</div>
-<div class="clear">&nbsp;</div>
-</div></div><div id="patternTopBar">
-<div id="patternTopBarContentsWrapper">
-<div id="patternTopBarContents"><table border="0" cellpadding="0" cellspacing="0" style="width:100%" summary="">
-<tr><td valign="middle"><span id="foswikiLogo" class="foswikiImage"><a href="WebHome.html"><img src="../pub/Main/WebPreferences/psi_logo_150.gif" border="0" alt="Paul Scherrer Institut" style="border:none; margin: -8px 0 0 15px;" /></a></span></td>
-<td align="right" valign="top" class="patternMetaMenu" id="psimetanav">
-<p></p> <ul>
-<li> <form name="quickSearchForm" id="solrSearchForm" action="https://intranet.psi.ch/PSI/Search"><input type="hidden" name="filter" value="web:MUSR" /><input type="text" class="foswikiInputField" id="quickSearchBox" name="search" value="" size="18" /><input type="hidden" name="scope" value="all" /><!-- <input type="hidden" name="web" value="MUSR" /> --> <noscript>&nbsp;<input type="submit" size="5" class="foswikiButton" name="submit" value="Search" />&nbsp;</noscript><input type="image" class="searchsubmit" alt="Search" value="Suche..." name="sa" src="../webbase/img/search.png">	</form>
-</li> <li> <form name="changeLanguage"    action="https://intranet.psi.ch/wiki/bin/oops/MUSR/Msr2Data" method="get">    <input type="hidden" name="redirectto" value="/MUSR/Msr2Data?cover=print" />    <select name="language" class="foswikiSelect"        onchange="document.changeLanguage.submit()">    <option  value="de">Deutsch</option> <option selected="selected" value="en">English</option></select>    <input type="hidden" name="template" value="oopslanguagechanged" />    <noscript>        <input class="foswikiButton" type="submit"            value="Change language" />    </noscript> </form>
-</li></ul> 
-<p></p>
-<p></p>
-<p></p>
-</td></tr></table>
-</div><!--/patternTopBarContents-->
-</div><!--/patternTopBarContentsWrapper-->
-</div><!-- /patternTopBar--><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar">Ideas, requests, problems regarding <a href="https://intranet.psi.ch/Main/WebHome">PSI Wiki</a>? <a href="mailto&#58;psi&#46;intranet&#64;psi&#46;ch&#63;subject&#61;PSI&#32;Wiki&#37;20Feedback&#37;20on&#37;20MUSR&#46;Msr2Data">Send feedback</a></div></div></div>
+<br class="imageClear" clear="all"/><div class="foswikiAttachments">
+<div class="twistyPlugin foswikiMakeVisible"><span id="topicattachmentslist1show" style="display:none" class="twistyRememberSetting twistyTrigger foswikiUnvisited twistyInited"><a class="patternTwistyButton" href="#"><img src="../pub/System/DocumentGraphics/toggleopen.png" border="0" alt="" /><span class="foswikiLinkLabel foswikiUnvisited">Attachments <span class='foswikiSmall foswikiGrayText'>1</span></span></a></span><span id="topicattachmentslist1hide" style="display:none" class="twistyRememberSetting twistyTrigger foswikiUnvisited twistyInited"><a class="patternTwistyButton" href="#"><img src="../pub/System/DocumentGraphics/toggleclose.png" border="0" alt="" /><span class="foswikiLinkLabel foswikiUnvisited">Attachments <span class='foswikiSmall foswikiGrayText'>1</span></span></a></span></div><div class="twistyPlugin"><div id="topicattachmentslist1toggle" style="" class="twistyRememberSetting twistyContent twistyInited">
+<table border="1" class="foswikiTable" id="tableMsr2Data1" rules="none" summary="Topic attachments"><caption>Topic attachments</caption>
+	<thead>
+		<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<th class="foswikiTableCol0 foswikiFirstCol"> <a href="https://intranet.psi.ch/MUSR/Msr2Data?cover=print;sortcol=0;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">I</a> </th>
+			<th class="foswikiTableCol1"> <a href="https://intranet.psi.ch/MUSR/Msr2Data?cover=print;sortcol=1;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Attachment</a> </th>
+			<th class="foswikiTableCol2"> <a href="https://intranet.psi.ch/MUSR/Msr2Data?cover=print;sortcol=2;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Action</a> </th>
+			<th class="foswikiTableCol3"> <a href="https://intranet.psi.ch/MUSR/Msr2Data?cover=print;sortcol=3;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Size</a> </th>
+			<th class="foswikiTableCol4"> <a href="https://intranet.psi.ch/MUSR/Msr2Data?cover=print;sortcol=4;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Date</a> </th>
+			<th class="foswikiTableCol5"> <a href="https://intranet.psi.ch/MUSR/Msr2Data?cover=print;sortcol=5;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Who</a> </th>
+			<th class="foswikiTableCol6 foswikiLastCol"> <a href="https://intranet.psi.ch/MUSR/Msr2Data?cover=print;sortcol=6;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Comment</a> </th>
+		</tr>
+	</thead>
+	<tbody>
+		<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='msr2data-input-tabs.png' /></span><span class="foswikiHidden">png</span> </td>
+			<td class="foswikiTableCol1 foswikiLast"> <a href="../pub/MUSR/Msr2Data/msr2data-input-tabs.png">msr2data-input-tabs.png</a> </td>
+			<td class="foswikiTableCol2 foswikiLast"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/Msr2Data?filename=msr2data-input-tabs.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
+			<td class="foswikiTableCol3 foswikiLast" style="text-align:right"> 36 K </td>
+			<td class="foswikiTableCol4 foswikiLast"> <span class="foswikiNoBreak">20 Jul 2011 - 12:13</span> </td>
+			<td class="foswikiTableCol5 foswikiLast"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
+			<td class="foswikiTableCol6 foswikiLastCol foswikiLast"> graphical interface to msr2data </td>
+		</tr>
+	</tbody></table>
+</div></div></div></div>
+<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span><a class="foswikiCurrentWebHomeLink" href="WebHome.html">WebHome</a> &gt; <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>Msr2Data <br />
+Topic revision:  <span class='patternRevInfo'>28 Apr 2016, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
 </div>
 </div>
 </div>
-</div></body>
-<!-- Mirrored from intranet.psi.ch/MUSR/Msr2Data?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 18 Dec 2014 13:46:37 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=iso-8859-1"><!-- /Added by HTTrack -->
-</html>
+</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar"><span class="foswikiRight"> <a href="http://foswiki.org/"><img src="../pub/System/ProjectLogos/foswiki-badge.png" alt="This site is powered by Foswiki" title="This site is powered by Foswiki" /></a></span>Copyright &copy; by the contributing authors. All material on this collaboration platform is the property of the contributing authors. <br /> Ideas, requests, problems regarding PSI Wiki? <a href='mailto:thomas.buecklers@psi.ch?subject=PSI Wiki %20Feedback%20on%20MUSR.Msr2Data'>Send feedback</a></div></div></div>
+</div>
+</div>
+</div>
+</div></div><!-- /endWrap -->
 <p></p>
-<p></p>
-<p></p>
-<p></p>
+<!-- Piwik -->
+
+<noscript><p><img src="../piwik/piwikf832.gif?idsite=7" style="border:0" alt=""></p></noscript>
+<!-- End Piwik Tag -->
+
+
+</body>
+
+<!-- Mirrored from intranet.psi.ch/MUSR/Msr2Data?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:26 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+</html>

doc/html/user/MUSR/MusrFitAcknowledgements.html

@@ -1,35 +1,38 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en_US" lang="en_US">
+<!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/MusrFitAcknowledgements?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 18 Dec 2014 13:46:11 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=iso-8859-1"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/MusrFitAcknowledgements?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:02 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
 <head>
 <link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
-<title>   MUSR :: MusrFitAcknowledgements</title>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+<title> MUSR :: MusrFitAcknowledgements</title>
+<meta http-equiv="X-UA-Compatible" content="IE=edge" />
+<meta charset="utf-8" />
+<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1.5, user-scalable=yes" />
+<meta name="mobile-web-app-capable" content="yes" />
+<meta name="mobile-web-app-status-bar-style" content="black-translucent" />
+<meta name="apple-mobile-web-app-capable" content="yes" />
+<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
 <link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
 <link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrFitAcknowledgements?t=1418910330" type="application/x-wiki" title="edit MusrFitAcknowledgements" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrFitAcknowledgements?t=1481904044" type="application/x-wiki" title="edit MusrFitAcknowledgements" />
 <meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
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-<base  /><!--[if IE]></base><![endif]-->
-<link rel='stylesheet' href='../pub/System/ImagePlugin/style.css' media='all' />
+<base  /><!--[if IE]></base><![endif]--><link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
+<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
+<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
+<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
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-</style>
-<style type="text/css" media="all">
-@import url('../pub/System/PatternSkinTheme2009/layout.css');
+@import url('../pub/System/PatternSkinTheme/layout.css');
 @import url('../pub/System/PatternSkinTheme2009/style.css');
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-@import url('../pub/System/PatternSkinTheme2009/column_left.css');
-@import url('../pub/System/PatternSkinTheme2009/variant_twiki.css');
-</style><style type="text/css" media="all">
+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/column_left.css' media='all' type='text/css' />
+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/variant_twiki.css' media='all' type='text/css' /><style type="text/css" media="all">
 	/* Styles that are set using variables */
 	.patternBookView .foswikiTopRow,
-	.patternWebIndicator a img,
-	.patternWebIndicator a:hover img {
+	.patternWebIndicator,
+	.patternWebIndicator a {
 		background-color:#D0D0D0;
 	}
 	#patternTopBarContents { background-image:url(../pub/System/PatternSkin/header5.gif); background-repeat:repeat-x;}
@@ -50,14 +53,8 @@
 	
 
 
-<style type="text/css" media="all">
-	@import url("../pub/System/PatternSkin/print.css");
-</style>
-<!--[if IE]><style type="text/css" media="screen">
-pre {
-	height:1%;
-	overflow-x:auto;
-}
+<link rel='stylesheet' href='../pub/System/PatternSkin/print.css' media='all' type='text/css' />
+<!--[if IE 7 ]><style type="text/css" media="screen">
 .foswikiAttachments,
 .foswikiForm,
 .foswikiHelp,
@@ -79,7 +76,17 @@ pre {
 .foswikiFormStep {
 	height:100%;
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-#foswikiLogin,
+#foswikiLogin {
+	 margin-left: 25%;
+	 margin-right: 25%;
+}
+#foswikiLogin .foswikiFormSteps {
+	 width:auto;
+}
+#foswikiLogin input[type="text"],
+#foswikiLogin input[type="password"] {
+	 width: auto;
+}
 .patternShadow {
 	border:10px solid #fff;
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-#foswikiLogin,
-.patternShadow {
-	border:10px solid #fff;
-	margin-top:10px;
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-<link rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
-</head>
-<body class="foswikiNoJs patternViewPage">
-<a name="PageTop"></a><div class="foswikiPage"><div id="patternScreen">
+<!--[if lte IE 9]>
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+<![endif]-->
+<!--[if gt IE 9]><!-->
+
+<!--<![endif]-->
+<!--JQUERYPLUGIN-->
+<!--JQUERYPLUGIN::MIGRATE-->
+<!--JQUERYPLUGIN::LIVEQUERY-->
+<!--JQUERYPLUGIN::FOSWIKI-->
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+<!--JavascriptFiles/foswikiPref-->
+<!--JavascriptFiles/foswikiForm-->
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-</div><div class="patternContent"><div class="foswikiTopic"><h1><a name="Acknowledgements_45_61_61musrfit_61_61"></a>  Acknowledgements - <code><b>musrfit</b></code> </h1>
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+<div class="patternContent"><div class="foswikiTopic"> <h1 id="Acknowledgements_45_61_61musrfit_61_61">  Acknowledgements - <code><b>musrfit</b></code> </h1>
 <p></p> <dl>
-<dt> Bastian M. Wojek </dt><dd> I am very much indebted to <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> for his rigorous testing of <code><a href="MusrFit.html">musrfit</a></code>, his many useful suggestions, contributions, and for the largest part of the <a href="WebHome.html" class="foswikiCurrentWebHomeLink">user manual of <code>musrfit</code></a> which makes it accessible to a broader audience! Many thanks Bastian!
-</dd></dl> 
+<dt> Bastian M. Wojek </dt><dd> I am very much indebted to <a href="http://www.fsf.org/register_form?referrer=8369">BMW</a> for his rigorous testing of <code><a href="MusrFit.html">musrfit</a></code>, his many useful suggestions, contributions, and for the largest part of the <a class="foswikiCurrentWebHomeLink" href="WebHome.html">user manual of <code>musrfit</code></a> which makes it accessible to a broader audience! Many thanks Bastian!
+</dd></dl> </div>
+<p></p>
 <p></p>
--- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> &amp; <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a> </div>
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-</li> <li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/psi.png" width="16" height="16" alt="psi" /></span> <a href="https://intranet.psi.ch/Main/WebList">weitere Webs</a>
-</li></ul> 
-<hr />
-<b>System Webs</b> <ul>
-<li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/foswiki.png" width="16" height="16" alt="foswiki" /></span> <a href="https://intranet.psi.ch/Sandbox/WebHome">Sandbox</a>
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-</li></ul> 
-<hr /> <ul>
-<li> <a href="https://intranet.psi.ch/MUSR/WebCreateNewTopic?parent=MusrFitAcknowledgements" target="_top"><span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/newtopic.png" width="16" height="16" alt="newtopic" /></span> Create New Topic</a> 
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-<p></p>
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-</div><!--/patternTopBarContents-->
-</div><!--/patternTopBarContentsWrapper-->
-</div><!-- /patternTopBar--><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar">Ideas, requests, problems regarding <a href="https://intranet.psi.ch/Main/WebHome">PSI Wiki</a>? <a href="mailto&#58;psi&#46;intranet&#64;psi&#46;ch&#63;subject&#61;PSI&#32;Wiki&#37;20Feedback&#37;20on&#37;20MUSR&#46;MusrFitAcknowledgements">Send feedback</a></div></div></div>
+<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span><a class="foswikiCurrentWebHomeLink" href="WebHome.html">WebHome</a> &gt; <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>MusrFitAcknowledgements <br />
+Topic revision:  <span class='patternRevInfo'>03 Jul 2015, suter_a</span></div>
 </div>
 </div>
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+</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar"><span class="foswikiRight"> <a href="http://foswiki.org/"><img src="../pub/System/ProjectLogos/foswiki-badge.png" alt="This site is powered by Foswiki" title="This site is powered by Foswiki" /></a></span>Copyright &copy; by the contributing authors. All material on this collaboration platform is the property of the contributing authors. <br /> Ideas, requests, problems regarding PSI Wiki? <a href='mailto:thomas.buecklers@psi.ch?subject=PSI Wiki %20Feedback%20on%20MUSR.MusrFitAcknowledgements'>Send feedback</a></div></div></div>
+</div>
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doc/html/user/MUSR/MusrGui.html

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+<!DOCTYPE html><html lang="en">
 
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+<title> MUSR :: MusrGui</title>
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+<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1.5, user-scalable=yes" />
+<meta name="mobile-web-app-capable" content="yes" />
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+<meta name="apple-mobile-web-app-capable" content="yes" />
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+body .foswikiTable td {border-style:solid none; vertical-align:top}
+body .foswikiTable th {border-style:none solid; vertical-align:top; background-color:#d6d3cf; color:#000000}
+body .foswikiTable th a:link {color:#000000}
+body .foswikiTable th a:visited {color:#000000}
+body .foswikiTable th a:hover {color:#000000; background-color:#d6d3cf}
+body .foswikiTable th.foswikiSortedCol {background-color:#c4c1ba}
+body .foswikiTable tr.foswikiTableRowdataBg0 td {background-color:#ffffff}
+body .foswikiTable tr.foswikiTableRowdataBg0 td.foswikiSortedCol {background-color:#f7f7f6}
+body .foswikiTable tr.foswikiTableRowdataBg1 td {background-color:#f7f7f6}
+body .foswikiTable tr.foswikiTableRowdataBg1 td.foswikiSortedCol {background-color:#f0f0ee}
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+<style class='head TABLEPLUGIN_specific' type="text/css" media="all">
+body .foswikiTable#tableMusrGui1 td {vertical-align:middle; vertical-align:top}
+body .foswikiTable#tableMusrGui1 td.foswikiTableCol0 {text-align:left}
+body .foswikiTable#tableMusrGui1 td.foswikiTableCol1 {text-align:left}
+body .foswikiTable#tableMusrGui1 td.foswikiTableCol2 {text-align:left}
+body .foswikiTable#tableMusrGui1 td.foswikiTableCol3 {text-align:right}
+body .foswikiTable#tableMusrGui1 td.foswikiTableCol4 {text-align:left}
+body .foswikiTable#tableMusrGui1 td.foswikiTableCol5 {text-align:left}
+body .foswikiTable#tableMusrGui1 td.foswikiTableCol6 {text-align:left}
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+body .foswikiTable#tableMusrGui1 th {vertical-align:middle; background-color:#ffffff; color:#0066cc; text-align:left}
+body .foswikiTable#tableMusrGui1 th a:link {color:#0066cc}
+body .foswikiTable#tableMusrGui1 th a:visited {color:#0066cc}
+body .foswikiTable#tableMusrGui1 th a:hover {color:#0066cc; background-color:#ffffff}
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+body .foswikiTable#tableMusrGui1 tr.foswikiTableRowdataBg0 td.foswikiSortedCol {background-color:#f5f5f5}
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+<link class='head IMAGEPLUGIN' rel="stylesheet" href="../pub/System/ImagePlugin/style.css" type="text/css" media="all" /><!--IMAGEPLUGIN--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
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+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/column_left.css' media='all' type='text/css' />
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+<h1 id="A_61_61musredit_47_40musrgui_41_61_61">  <code><b>musredit / (musrgui)</b></code> </h1>
 <p></p>
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-      	
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-<h1><a name="A_61_61musrgui_47_musredit_61_61"></a>  <code><b>musrgui / musredit</b></code> </h1>
-<p></p>
-<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
-<li> <a href="MusrGui.html#A_61_61musrgui_47_musredit_61_61"> musrgui / musredit </a>
+<div class="foswikiToc" id="foswikiTOC"> <ul>
+<li> <a href="MusrGui.html#A_61_61musredit_47_40musrgui_41_61_61"> musredit / (musrgui) </a>
 </li> <li> <a href="MusrGui.html#A_1_Introduction"> 1  Introduction </a>
 </li> <li> <a href="MusrGui.html#A_2_Available_Executables_44_Configuration_Files_and_their_Basic_Usage"> 2  Available Executables, Configuration Files and their Basic Usage </a> <ul>
-<li> <a href="MusrGui.html#A_2.1_musrgui_47_musredit"> 2.1  musrgui / musredit </a>
-</li> <li> <a href="MusrGui.html#A_2.2_musrgui_startup.xml_47_musredit_startup.xml"> 2.2  musrgui_startup.xml / musredit_startup.xml </a>
+<li> <a href="MusrGui.html#A_2.1_musredit_47_40musrgui_41"> 2.1  musredit / (musrgui) </a>
+</li> <li> <a href="MusrGui.html#A_2.2_musredit_startup.xml_47_musrgui_startup.xml"> 2.2  musredit_startup.xml / musrgui_startup.xml </a>
 </li></ul> 
 </li> <li> <a href="MusrGui.html#A_3_61_61musrfit_61_61_Features"> 3  musrfit Features </a>
 </li> <li> <a href="MusrGui.html#A_4_Editor_Features"> 4  Editor Features </a>
@@ -131,15 +173,15 @@ pre {
 </li></ul> 
 </div>
 <p></p>
-<h1><a name="A_1_Introduction"></a> 1  Introduction </h1>
-<code>musrgui</code> and <code>musredit</code> are editors which also provide a graphical user interface to the programs contained in the <code><a href="MusrFit.html">musrfit</a></code> suite and are intended to help the user handle <code>musrfit</code> msr files. They are implemented in <code>C++</code> and use the <a href="http://qt.nokia.com/" target="_top">Qt</a> framework. Principally, <code>musrgui</code> and <code>musredit</code> are doing the same, but are based on different Qt versions. <code>musrgui</code> is based on Qt 3.x and will only be maintained on bug-fixing level since the Qt 3.x licensing is less straight forward than the Qt 4.x one. <code>musredit</code> is based on Qt 4.6 (or above) and this is the program which will be developed further.<br>
+<h1 id="A_1_Introduction"> 1  Introduction </h1>
+<code>musredit</code> and <code>musrgui</code> are editors which also provide a graphical user interface to the programs contained in the <code><a href="MusrFit.html">musrfit</a></code> suite and are intended to help the user handle <code>musrfit</code> msr files. They are implemented in <code>C++</code> and use the <a href="http://qt.nokia.com/">Qt</a> framework. Principally, <code>musrgui</code> and <code>musredit</code> are doing the same, but are based on different Qt versions. <code>musrgui</code> is based on Qt 3.x and will only be maintained on bug-fixing level since the Qt 3.x licensing is less straight forward than the Qt 4.x one. <code>musredit</code> is based on Qt 4.6 (or above) and this is the program which will be developed further.<br>
 On this documentation page only the features related to <code>musrfit</code> are described&mdash;the basic editor functions which should be self-explanatory are not.
 <strong><span class='foswikiRedFG'>Before going on using <code>musrgui</code> / <code>musredit</code> it is strongly recommended to read the <a href="MusrFit.html">manual</a> of <code>musrfit</code> first!</span></strong>
 <p></p>
-<h1><a name="A_2_Available_Executables_44_Configuration_Files_and_their_Basic_Usage"></a> 2  Available Executables, Configuration Files and their Basic Usage </h1>
-<a name="MusrEdit"></a>
-<h2><a name="A_2.1_musrgui_47_musredit"></a> 2.1  musrgui / musredit </h2>
-<code>musrgui</code> / <code>musredit</code> are the editor executables. If called from within a shell they accept a few optional parameters: <dl>
+<h1 id="A_2_Available_Executables_44_Configuration_Files_and_their_Basic_Usage"> 2  Available Executables, Configuration Files and their Basic Usage </h1>
+<span id="MusrEdit"></span>
+<h2 id="A_2.1_musredit_47_40musrgui_41"> 2.1  musredit / (musrgui) </h2>
+<code>musredit</code> / <code>musrgui</code> are the editor executables. If called from within a shell they accept a few optional parameters: <dl>
 <dt> &lt;msr_files&gt; </dt><dd> file names of the msr files that should be opened in separate editor tabs on startup of <code>musrgui</code> / <code>musredit</code>.
 </dd> <dt> --help </dt><dd> displays a small help notice in the shell explaining the basic usage of the program
 </dd> <dt> --version </dt><dd> prints the version number of <code>musrgui</code> / <code>musredit</code>
@@ -147,15 +189,15 @@ On this documentation page only the features related to <code>musrfit</code> are
 <p></p>
 If called without any parameters an empty editor window opens.
 <p></p>
-<a name="MusreditStartupXml"></a>
-<h2><a name="A_2.2_musrgui_startup.xml_47_musredit_startup.xml"></a> 2.2  musrgui_startup.xml / musredit_startup.xml </h2>
-<code><b>musrgui_startup.xml</b></code> / <code><b>musredit_startup.xml</b></code> are configuration files located at the <code>musrgui</code> / <code>musredit</code> binary path. It is also possible to have another version of this file in the working directory which then will be used!
+<span id="MusreditStartupXml"></span>
+<h2 id="A_2.2_musredit_startup.xml_47_musrgui_startup.xml"> 2.2  musredit_startup.xml / musrgui_startup.xml </h2>
+<code><b>musredit_startup.xml</b></code> / <code><b>musrgui_startup.xml</b></code> are configuration files located at the <code>musredit</code> / <code>musrgui</code> binary path. It is also possible to have another version of this file in the working directory which then will be used!
 <p></p>
-In this file the following XML tags are allowed to define settings and might proof useful for all users of <code>musrgui</code> / <code>musredit</code>: <dl>
+In this file the following XML tags are allowed to define settings and might proof useful for all users of <code>musredit</code> / <code>musrgui</code>: <dl>
 <dt> &lt;general&gt;&lt;/general&gt; </dt><dd> set the default paths to executables and files in this environment <dl>
 <dt> &lt;exec_path&gt;PATH_TO_EXEC&lt;/exec_path&gt; </dt><dd> set the path <strong>PATH_TO_EXEC</strong> where the executables <code>musrfit</code>, <code>musrview</code>, <code>musrt0</code>, etc. can be found (inside the &lt;general&gt; environment)
 </dd> <dt> &lt;default_save_path&gt;SAV_PATH&lt;/default_save_path&gt; </dt><dd> specify the path <strong>SAV_PATH</strong> where <code>musrgui</code> / <code>musredit</code> point by default when opening and saving msr files (inside the &lt;general&gt; environment)
-</dd> <dt> &lt;msr_default_file_path&gt;MSR_DEF_PATH&lt;/msr_default_file_path&gt; </dt><dd> set the path <strong>MSR_DEF_PATH</strong> where the <a href="#MusrfitFeatures" class="foswikiCurrentTopicLink">default msr files provided by</a> <code>musrgui</code> are stored (inside the &lt;general&gt; environment)
+</dd> <dt> &lt;msr_default_file_path&gt;MSR_DEF_PATH&lt;/msr_default_file_path&gt; </dt><dd> set the path <strong>MSR_DEF_PATH</strong> where the <a class="foswikiCurrentTopicLink" href="#MusrfitFeatures">default msr files provided by</a> <code>musrgui</code> are stored (inside the &lt;general&gt; environment)
 </dd> <dt> &lt;title_from_data_file&gt;y/n&lt;/title_from_data_file&gt; </dt><dd> specify if <code>musrfit</code> should be called with the <a href="MusrFit.html#MusrFit">-t option</a> by default (inside the &lt;general&gt; environment)
 </dd> <dt> &lt;enable_musrt0&gt;y/n&lt;/enable_musrt0&gt; </dt><dd> specify if <code><a href="MusrFit.html#MusrT0">musrt0</a></code> can be called from within <code>musrgui</code> / <code>musredit</code> (inside the &lt;general&gt; environment)
 </dd></dl> 
@@ -264,143 +306,94 @@ An example of the <code><b>musrgui_startup.xml</b></code> looks like:
 &#60;/musrgui&#95;startup&#62;
 </pre>
 <p></p>
-<a name="MusrfitFeatures"></a>
-<h1><a name="A_3_61_61musrfit_61_61_Features"></a> 3  <code><b>musrfit</b></code> Features </h1>
+<span id="MusrfitFeatures"></span>
+<h1 id="A_3_61_61musrfit_61_61_Features"> 3  <code><b>musrfit</b></code> Features </h1>
 The features of <code>musrfit</code> which can be accessed by the graphical front ends <code>musrgui</code> / <code>musredit</code> are described in the following. All functions can either be called by choosing them from the MusrFit menu, by clicking the respective button in the MusrFit bar, or by using a keyboard shortcut.
-<p></p> <dl>
-<dt> <img alt="musrasym.png" src="../pub/MUSR/MusrGui/musrasym.png" /> Asymmetry Default (Alt+a) </dt><dd> Generate a full msr file suitable for the <a href="MusrFit.html#FitTypes">fit type</a> <strong>2</strong> of <code>musrfit</code> from defaults. Calling this function opens a window where the relative path and file name to a data file as well as the file format that should be used have to be specified. For instance if the data file <code><b>/path-to-datadir/2007/lem07_his_8472.root</b></code> should be used and <code><b>/path-to-datadir</b></code> is on the path where <code>musrfit</code> <a href="MusrFit.html#PathToDataFiles">looks for data files</a> then the file name would be <code><b>2007/lem07_his_8472</b></code> and the file format either <strong>ROOT-NPP</strong> or <strong>ROOT-PPC</strong>.
-</dd></dl> 
-<p></p> <dl>
-<dt> <img alt="musrsinglehisto.png" src="../pub/MUSR/MusrGui/musrsinglehisto.png" /> Single-Histogram Default (Alt+h) </dt><dd> Generate a full msr file suitable for the <a href="MusrFit.html#FitTypes">fit type</a> <strong>0</strong> of <code>musrfit</code> from defaults. Calling this function opens a window where the relative path and file name to a data file as well as the file format that should be used have to be specified. For instance if the data file <code><b>/path-to-datadir/d2007/deltat_pta_gps_8472.bin</b></code> should be used and <code><b>/path-to-datadir</b></code> is on the path where <code>musrfit</code> <a href="MusrFit.html#PathToDataFiles">looks for data files</a> then the file name would be <code><b>d2007/deltat_pta_gps_8472</b></code> and the file format <strong>PSI-BIN</strong>.
-</dd></dl> 
-<p></p> <dl>
-<dt> <img alt="musrcalcchisq.png" src="../pub/MUSR/MusrGui/musrcalcchisq.png" /> Calculate Chisq (Alt+c) </dt><dd> <pre class="bash">musrfit &#60;msr&#95;file&#62; --chisq-only</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>.
-</dd></dl> 
-<p></p> <dl>
-<dt> <img alt="musrfit.png" src="../pub/MUSR/MusrGui/musrfit.png" /> Fit (Alt+f) </dt><dd> <pre class="bash">musrfit &#60;msr&#95;file&#62; &#91;optional parameters]</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. The optional parameters may be chosen under <a href="#MusrPrefs" class="foswikiCurrentTopicLink">Preferences</a>. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>.
-</dd></dl> 
-<p></p> <dl>
-<dt> <img alt="musrswap.png" src="../pub/MUSR/MusrGui/musrswap.png" /> Swap Msr &#8596; Mlog (Alt+s) </dt><dd> Swap the msr and mlog files. E.g., for a file called <code><b>8472_zf.msr</b></code>, this is copied to <code><b>8472_zf.mlog</b></code> and vice versa.
-</dd></dl> 
-<p></p> <dl>
-<dt> <img alt="musrmsr2data.png" src="../pub/MUSR/MusrGui/musrmsr2data.png" /> Msr2data (Alt+m) </dt><dd> Opens a graphical interface to the <code>msr2data</code> program described in detail in its own <a href="Msr2Data.html#MusrGuiInterface">manual</a>.
-</dd></dl> 
-<p></p> <dl>
-<dt> <img alt="musrview.png" src="../pub/MUSR/MusrGui/musrview.png" /> View (Alt+v) </dt><dd> <pre class="bash">musrview &#60;msr&#95;file&#62;</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrView">manual</a> of <code>musrfit</code>.
-</dd></dl> 
-<p></p> <dl>
-<dt> <img alt="musrt0.png" src="../pub/MUSR/MusrGui/musrt0.png" /> T0 (Alt+t) </dt><dd> <pre class="bash">musrt0 &#60;msr&#95;file&#62;</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrT0">manual</a> of <code>musrfit</code>.
-</dd></dl> 
 <p></p>
-<a name="MusrPrefs"></a> <dl>
-<dt> <img alt="musrprefs.png" src="../pub/MUSR/MusrGui/musrprefs.png" /> Preferences (Alt+p) </dt><dd> Opens a window in which the optional parameters that should be passed to <code>musrfit</code> can be chosen. These options are <code><b>--keep-mn2-output</b></code>, <code><b>--dump ascii</b></code>, <code><b>--dump root</b></code>, and <code><b>--title-from-data-file</b></code>. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>. Additionally, the access to <code>musrt0</code> can be enabled temporarily.
-</dd></dl> 
-<p></p> <dl>
-<dt> <img alt="musrdump.png" src="../pub/MUSR/MusrGui/musrdump.png" /> Dump Header </dt><dd> Opens a file dialog which allows to select a &mu;SR data file. When this file can be read, the run header info is dumped into a dialog window. Essentially this calls <code><b>dump_header</b></code> internally.
-</dd></dl> 
+   $ <img alt="musrasym.png" src="../pub/MUSR/MusrGui/musrasym.png" /> Asymmetry Default (Alt+a): Generate a full msr file suitable for the <a href="MusrFit.html#FitTypes">fit type</a> <strong>2</strong> of <code>musrfit</code> from defaults. Calling this function opens a window where the relative path and file name to a data file as well as the file format that should be used have to be specified. For instance if the data file <code><b>/path-to-datadir/2007/lem07_his_8472.root</b></code> should be used and <code><b>/path-to-datadir</b></code> is on the path where <code>musrfit</code> <a href="MusrFit.html#PathToDataFiles">looks for data files</a> then the file name would be <code><b>2007/lem07_his_8472</b></code> and the file format either <strong>ROOT-NPP</strong> or <strong>ROOT-PPC</strong>.
 <p></p>
-<a name="EditorFeatures"></a>
-<h1><a name="A_4_Editor_Features"></a> 4  Editor Features </h1>
+   $ <img alt="musrsinglehisto.png" src="../pub/MUSR/MusrGui/musrsinglehisto.png" /> Single-Histogram Default (Alt+h): Generate a full msr file suitable for the <a href="MusrFit.html#FitTypes">fit type</a> <strong>0</strong> of <code>musrfit</code> from defaults. Calling this function opens a window where the relative path and file name to a data file as well as the file format that should be used have to be specified. For instance if the data file <code><b>/path-to-datadir/d2007/deltat_pta_gps_8472.bin</b></code> should be used and <code><b>/path-to-datadir</b></code> is on the path where <code>musrfit</code> <a href="MusrFit.html#PathToDataFiles">looks for data files</a> then the file name would be <code><b>d2007/deltat_pta_gps_8472</b></code> and the file format <strong>PSI-BIN</strong>.
+<p></p>
+   $ <img alt="musrcalcchisq.png" src="../pub/MUSR/MusrGui/musrcalcchisq.png" /> Calculate Chisq (Alt+c): <pre class="bash">musrfit &#60;msr&#95;file&#62; --chisq-only</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>.
+<p></p>
+   $ <img alt="musrfit.png" src="../pub/MUSR/MusrGui/musrfit.png" /> Fit (Alt+f): <pre class="bash">musrfit &#60;msr&#95;file&#62; &#91;optional parameters&#93;</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. The optional parameters may be chosen under <a class="foswikiCurrentTopicLink" href="#MusrPrefs">Preferences</a>. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>.
+<p></p>
+   $ <img alt="musrswap.png" src="../pub/MUSR/MusrGui/musrswap.png" /> Swap Msr &#8596; Mlog (Alt+s): Swap the msr and mlog files. E.g., for a file called <code><b>8472_zf.msr</b></code>, this is copied to <code><b>8472_zf.mlog</b></code> and vice versa.
+<p></p>
+   $ <img alt="musrmsr2data.png" src="../pub/MUSR/MusrGui/musrmsr2data.png" /> Msr2data (Alt+m): Opens a graphical interface to the <code>msr2data</code> program described in detail in its own <a href="Msr2Data.html#MusrGuiInterface">manual</a>.
+<p></p>
+   $ <img alt="musrview.png" src="../pub/MUSR/MusrGui/musrview.png" /> View (Alt+v): <pre class="bash">musrview &#60;msr&#95;file&#62;</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrView">manual</a> of <code>musrfit</code>.
+<p></p>
+   $ <img alt="musrt0.png" src="../pub/MUSR/MusrGui/musrt0.png" /> T0 (Alt+t): <pre class="bash">musrt0 &#60;msr&#95;file&#62;</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrT0">manual</a> of <code>musrfit</code>.
+<p></p>
+   $ <img alt="musrFT.png" src="../pub/MUSR/MusrGui/musrFT.png" /> Raw Fourier: <code>musrFT &lt;with-many-options&gt;</code> is called. For a proper documentation of it, check the <a href="MusrFit.html#MusrFT">manual</a> of <code>musrFT</code>.
+<p></p>
+<span id="MusrPrefs"></span>
+   $ <img alt="musrprefs.png" src="../pub/MUSR/MusrGui/musrprefs.png" /> Preferences (Alt+p): Opens a window in which the optional parameters that should be passed to <code>musrfit</code> can be chosen. These options are <code><b>--keep-mn2-output</b></code>, <code><b>--dump ascii</b></code>, <code><b>--dump root</b></code>, and <code><b>--title-from-data-file</b></code>. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>. Additionally, the access to <code>musrt0</code> can be enabled temporarily.
+<p></p>
+   $ <img alt="musrdump.png" src="../pub/MUSR/MusrGui/musrdump.png" /> Dump Header: Opens a file dialog which allows to select a &mu;SR data file. When this file can be read, the run header info is dumped into a dialog window. Essentially this calls <code><b>dump_header</b></code> internally.
+<p></p>
+<span id="EditorFeatures"></span>
+<h1 id="A_4_Editor_Features"> 4  Editor Features </h1>
 Besides the functions described above and which are mostly interfacing <code>musrfit/msr2data</code> the editors of <code>musrgui</code> / <code>musredit</code> offer various functions for manipulating especially <code>musrfit</code> msr files:
-<img src="../pub/MUSR/MusrGui/musrgui-editor-v0.png" alt="musrgui editor features" width='415' height='566' align="right" /> <ul>
+<img class='imagePlain imagePlain_right ' src='../pub/MUSR/MusrGui/igp_4e5811420d6b5b31cac70e88b8477a14_musrgui-editor-v0.png' alt='musrgui editor features' title='musrgui-editor-v0.png' width='415' height='566'   style='' /> <ul>
 <li> Upon right-clicking an open msr file a menu as shown to the right is displayed which offers the addition of any valid msr file block or theory function. In case a simple theory function is chosen, the function will be inserted into the THEORY block using the <a href="MusrFit.html#TheoryTable">correct syntax</a>. If one chooses to add a whole block to the file a dialog opens in which the necessary information for each block as described in the <a href="MusrFit.html#DescriptionOfTheMsrFileFormat">manual</a> of <code>musrfit</code> can be supplied. <span class='foswikiBlueFG'>This feature is available only in <code>musrgui</code>. In <code>musredit</code> the respective functions can be accessed through the <em>Edit</em> menu.</span>
 </li> <li> In order to comment or uncomment lines in a msr file select the according lines and apply <strong>Edit &rarr; (Un)Comment</strong> or use the keyboard shortcut <strong>Ctrl+(Shift)+m</strong>.
 </li></ul> 
 <p></p>
-<a name="BugTracking"></a>
-<h1><a name="A_5_Bugtracking"></a> 5  Bugtracking </h1>
+<span id="BugTracking"></span>
+<h1 id="A_5_Bugtracking"> 5  Bugtracking </h1>
 <p></p>
-For reporting bugs or requesting new features and improvements please use the <a href="https://tracker.intranet.psi.ch/jira/browse/MUSR" target="_top">PSI Tracker</a> or send an e-mail to A. Suter.
+For reporting bugs or requesting new features and improvements please use the <a href="https://bitbucket.org/muonspin/musrfit/issues">Bitbucket Tracker</a>,  <a href="https://tracker.psi.ch/jira/browse/MUSR/">PSI Tracker</a> (PSI account needed) or send an e-mail to A. Suter.
 <p></p>
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-<div class="foswikiContentFooter"></div><!-- -->
-<!-- -->
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-<a name="topic-actions"></a>
-  <div class="patternTopicActions foswikiFormStep">
-	 <span class="patternActionButtons"><span><a href='https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrGui?t=1418910327' rel='nofollow' title='Edit this topic text' accesskey='e'><span class='foswikiAccessKey'>E</span>dit</a></span><span class='foswikiSeparator'>&nbsp;|&nbsp;</span><span class="foswikiRequiresChangePermission"><a href='https://intranet.psi.ch/wiki/bin/attach/MUSR/MusrGui' rel='nofollow' title='Attach an image or document to this topic' accesskey='a'><span class='foswikiAccessKey'>A</span>ttach</a></span><span class='foswikiSeparator'>&nbsp;|&nbsp;</span><span><a href='MusrGuic99a.html?cover=print;cover=print' rel='nofollow' title='Printable version of this topic' accesskey='p'><span class='foswikiAccessKey'>P</span>rint version</a></span><span class='foswikiSeparator'>&nbsp;|&nbsp;</span><span><a href='https://intranet.psi.ch/print/php/pdf.php?url=MUSR/MusrGui?cover=print' title='PDF version of this topic'>PDF</a></span><span class='foswikiSeparator'>&nbsp;|&nbsp;</span><span><span class="foswikiRequiresChangePermission"><a href='https://intranet.psi.ch/wiki/bin/oops/MUSR/MusrGui?template=oopshistory' rel='nofollow' title='View total topic history' accesskey='h'><span class='foswikiAccessKey'>H</span>istory</a></span>: r19&nbsp;<a rel="nofollow" href="https://intranet.psi.ch/wiki/bin/compare/MUSR/MusrGui?rev1=18;rev2=19">&lt;</a>&nbsp;<a rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrGui?rev=18">r18</a>&nbsp;<a rel="nofollow" href="https://intranet.psi.ch/wiki/bin/compare/MUSR/MusrGui?rev1=17;rev2=18">&lt;</a>&nbsp;<a rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrGui?rev=17">r17</a>&nbsp;<a rel="nofollow" href="https://intranet.psi.ch/wiki/bin/compare/MUSR/MusrGui?rev1=16;rev2=17">&lt;</a>&nbsp;<a rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrGui?rev=16">r16</a></span><span class='foswikiSeparator'>&nbsp;|&nbsp;</span><span><a href='https://intranet.psi.ch/MUSR/MusrGui?template=backlinksweb' rel='nofollow' title='Search the MUSR Web for topics that link to here' accesskey='b'><span class='foswikiAccessKey'>B</span>acklinks</a></span><span class='foswikiSeparator'>&nbsp;|&nbsp;</span><span><a href='https://intranet.psi.ch/MUSR/MusrGui?raw=on' rel='nofollow' title='View without formatting' accesskey='v'><span class='foswikiAccessKey'>V</span>iew wiki text</a></span><span class='foswikiSeparator'>&nbsp;|&nbsp;</span><span><a href='https://intranet.psi.ch/MUSR/MusrGui?refresh=on' title='Refresh images and LaTeX charts'>Refresh</a></span><span class='foswikiSeparator'>&nbsp;|&nbsp;</span><span><a href='https://intranet.psi.ch/MUSR/MusrGui?template=more&amp;maxrev=19&amp;currrev=19' rel='nofollow' title='Delete or rename this topic; set parent topic; view and compare revisions' accesskey='m'><span class='foswikiAccessKey'>M</span>ore topic actions</a></span></span>
-  </div>
-</div></div><div class="patternInfo"><span class="patternRevInfo">Topic revision: r19 - 25 May 2012, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
-</div>
-</div><div id="patternSideBar"><div id="patternClearHeaderLeft"></div>
-<div id="patternSideBarContents">
-<div class="patternLeftBarPersonal">
-<ul><li class="patternLogIn"><a href="https://intranet.psi.ch/wiki/bin/logon/MUSR/MusrGui">Log In</a> or <a href="https://intranet.psi.ch/System/UserRegistration">Register</a></li></ul>
-</div>
+--  <a href="http://www.psi.ch/low-energy-muons/people">AS</a> &amp; <a href="http://www.fsf.org/register_form?referrer=8369">BMW</a></div>
 <p></p>
 <p></p>
-<b>PSI Webs</b> <ul>
-<li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/psi.png" width="16" height="16" alt="psi" /></span> <a href="https://intranet.psi.ch/Main/WebHome">Main</a>
-</li> <li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/psi.png" width="16" height="16" alt="psi" /></span> <a href="https://intranet.psi.ch/Main/WebList">weitere Webs</a>
-</li></ul> 
-<hr />
-<b>System Webs</b> <ul>
-<li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/foswiki.png" width="16" height="16" alt="foswiki" /></span> <a href="https://intranet.psi.ch/Sandbox/WebHome">Sandbox</a>
-</li> <li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/foswiki.png" width="16" height="16" alt="foswiki" /></span> <a href="https://intranet.psi.ch/System/WebHome">Documentation</a>
-</li></ul> 
-<hr /> <ul>
-<li> <a href="https://intranet.psi.ch/MUSR/WebCreateNewTopic?parent=MusrGui" target="_top"><span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/newtopic.png" width="16" height="16" alt="newtopic" /></span> Create New Topic</a> 
-</li> <li> <a href="WebTopicList.html"> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/index.png" width="16" height="16" alt="index" /></span> Show All Topics</a> 
-</li> <li> <a href="WebSearch.html"> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/searchtopic.png" width="16" height="16" alt="searchtopic" /></span> Search in Topics</a> 
-</li> <li> <a href="WebChanges.html"> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/changes.png" width="16" height="16" alt="changes" /></span> Recent Changes</a>
-</li> <li> <a href="WebNotify.html"> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/notify.png" width="16" height="16" alt="notify" /></span> Define Notifications</a>
-</li></ul> 
-<p></p>
-</div></div>
-</div>
-<div class="clear">&nbsp;</div>
-</div></div><div id="patternTopBar">
-<div id="patternTopBarContentsWrapper">
-<div id="patternTopBarContents"><table border="0" cellpadding="0" cellspacing="0" style="width:100%" summary="">
-<tr><td valign="middle"><span id="foswikiLogo" class="foswikiImage"><a href="WebHome.html"><img src="../pub/Main/WebPreferences/psi_logo_150.gif" border="0" alt="Paul Scherrer Institut" style="border:none; margin: -8px 0 0 15px;" /></a></span></td>
-<td align="right" valign="top" class="patternMetaMenu" id="psimetanav">
-<p></p> <ul>
-<li> <form name="quickSearchForm" id="solrSearchForm" action="https://intranet.psi.ch/PSI/Search"><input type="hidden" name="filter" value="web:MUSR" /><input type="text" class="foswikiInputField" id="quickSearchBox" name="search" value="" size="18" /><input type="hidden" name="scope" value="all" /><!-- <input type="hidden" name="web" value="MUSR" /> --> <noscript>&nbsp;<input type="submit" size="5" class="foswikiButton" name="submit" value="Search" />&nbsp;</noscript><input type="image" class="searchsubmit" alt="Search" value="Suche..." name="sa" src="../webbase/img/search.png">	</form>
-</li> <li> <form name="changeLanguage"    action="https://intranet.psi.ch/wiki/bin/oops/MUSR/MusrGui" method="get">    <input type="hidden" name="redirectto" value="/MUSR/MusrGui?cover=print" />    <select name="language" class="foswikiSelect"        onchange="document.changeLanguage.submit()">    <option  value="de">Deutsch</option> <option selected="selected" value="en">English</option></select>    <input type="hidden" name="template" value="oopslanguagechanged" />    <noscript>        <input class="foswikiButton" type="submit"            value="Change language" />    </noscript> </form>
-</li></ul> 
-<p></p>
-<p></p>
-<p></p>
-</td></tr></table>
-</div><!--/patternTopBarContents-->
-</div><!--/patternTopBarContentsWrapper-->
-</div><!-- /patternTopBar--><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar">Ideas, requests, problems regarding <a href="https://intranet.psi.ch/Main/WebHome">PSI Wiki</a>? <a href="mailto&#58;psi&#46;intranet&#64;psi&#46;ch&#63;subject&#61;PSI&#32;Wiki&#37;20Feedback&#37;20on&#37;20MUSR&#46;MusrGui">Send feedback</a></div></div></div>
+<br class="imageClear" clear="all"/><div class="foswikiAttachments">
+<div class="twistyPlugin foswikiMakeVisible"><span id="topicattachmentslist1show" style="display:none" class="twistyRememberSetting twistyTrigger foswikiUnvisited twistyInited"><a class="patternTwistyButton" href="#"><img src="../pub/System/DocumentGraphics/toggleopen.png" border="0" alt="" /><span class="foswikiLinkLabel foswikiUnvisited">Attachments <span class='foswikiSmall foswikiGrayText'>1</span></span></a></span><span id="topicattachmentslist1hide" style="display:none" class="twistyRememberSetting twistyTrigger foswikiUnvisited twistyInited"><a class="patternTwistyButton" href="#"><img src="../pub/System/DocumentGraphics/toggleclose.png" border="0" alt="" /><span class="foswikiLinkLabel foswikiUnvisited">Attachments <span class='foswikiSmall foswikiGrayText'>1</span></span></a></span></div><div class="twistyPlugin"><div id="topicattachmentslist1toggle" style="" class="twistyRememberSetting twistyContent twistyInited">
+<table border="1" class="foswikiTable" id="tableMusrGui1" rules="none" summary="Topic attachments"><caption>Topic attachments</caption>
+	<thead>
+		<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<th class="foswikiTableCol0 foswikiFirstCol"> <a href="https://intranet.psi.ch/MUSR/MusrGui?cover=print;sortcol=0;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">I</a> </th>
+			<th class="foswikiTableCol1"> <a href="https://intranet.psi.ch/MUSR/MusrGui?cover=print;sortcol=1;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Attachment</a> </th>
+			<th class="foswikiTableCol2"> <a href="https://intranet.psi.ch/MUSR/MusrGui?cover=print;sortcol=2;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Action</a> </th>
+			<th class="foswikiTableCol3"> <a href="https://intranet.psi.ch/MUSR/MusrGui?cover=print;sortcol=3;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Size</a> </th>
+			<th class="foswikiTableCol4"> <a href="https://intranet.psi.ch/MUSR/MusrGui?cover=print;sortcol=4;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Date</a> </th>
+			<th class="foswikiTableCol5"> <a href="https://intranet.psi.ch/MUSR/MusrGui?cover=print;sortcol=5;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Who</a> </th>
+			<th class="foswikiTableCol6 foswikiLastCol"> <a href="https://intranet.psi.ch/MUSR/MusrGui?cover=print;sortcol=6;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Comment</a> </th>
+		</tr>
+	</thead>
+	<tbody>
+		<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='musrgui-editor-v0.png' /></span><span class="foswikiHidden">png</span> </td>
+			<td class="foswikiTableCol1 foswikiLast"> <a href="../pub/MUSR/MusrGui/musrgui-editor-v0.png">musrgui-editor-v0.png</a> </td>
+			<td class="foswikiTableCol2 foswikiLast"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/MusrGui?filename=musrgui-editor-v0.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
+			<td class="foswikiTableCol3 foswikiLast" style="text-align:right"> 37 K </td>
+			<td class="foswikiTableCol4 foswikiLast"> <span class="foswikiNoBreak">10 Apr 2009 - 14:53</span> </td>
+			<td class="foswikiTableCol5 foswikiLast"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
+			<td class="foswikiTableCol6 foswikiLastCol foswikiLast"> musrgui options available upon right clicking a open msr-file </td>
+		</tr>
+	</tbody></table>
+</div></div></div></div>
+<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span><a class="foswikiCurrentWebHomeLink" href="WebHome.html">WebHome</a> &gt; <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>MusrGui <br />
+Topic revision:  <span class='patternRevInfo'>19 Feb 2015, suter_a</span></div>
 </div>
 </div>
 </div>
-</div></body>
-<!-- Mirrored from intranet.psi.ch/MUSR/MusrGui?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 18 Dec 2014 13:46:09 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=iso-8859-1"><!-- /Added by HTTrack -->
-</html>
+</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar"><span class="foswikiRight"> <a href="http://foswiki.org/"><img src="../pub/System/ProjectLogos/foswiki-badge.png" alt="This site is powered by Foswiki" title="This site is powered by Foswiki" /></a></span>Copyright &copy; by the contributing authors. All material on this collaboration platform is the property of the contributing authors. <br /> Ideas, requests, problems regarding PSI Wiki? <a href='mailto:thomas.buecklers@psi.ch?subject=PSI Wiki %20Feedback%20on%20MUSR.MusrGui'>Send feedback</a></div></div></div>
+</div>
+</div>
+</div>
+</div></div><!-- /endWrap -->
 <p></p>
-<p></p>
-<p></p>
-<p></p>
+<!-- Piwik -->
+
+<noscript><p><img src="../piwik/piwikf832.gif?idsite=7" style="border:0" alt=""></p></noscript>
+<!-- End Piwik Tag -->
+
+
+</body>
+
+<!-- Mirrored from intranet.psi.ch/MUSR/MusrGui?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:01 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+</html>

doc/html/user/MUSR/QuickStart.html

@@ -1,35 +1,38 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en_US" lang="en_US">
+<!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/QuickStart?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 18 Dec 2014 13:46:03 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=iso-8859-1"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/QuickStart?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:00:58 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
 <head>
 <link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
-<title>   MUSR :: QuickStart</title>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+<title> MUSR :: QuickStart</title>
+<meta http-equiv="X-UA-Compatible" content="IE=edge" />
+<meta charset="utf-8" />
+<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1.5, user-scalable=yes" />
+<meta name="mobile-web-app-capable" content="yes" />
+<meta name="mobile-web-app-status-bar-style" content="black-translucent" />
+<meta name="apple-mobile-web-app-capable" content="yes" />
+<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
 <link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
 <link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/QuickStart?t=1418910326" type="application/x-wiki" title="edit QuickStart" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/QuickStart?t=1481904043" type="application/x-wiki" title="edit QuickStart" />
 <meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
 <meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
 <meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
-<base  /><!--[if IE]></base><![endif]-->
-<link rel='stylesheet' href='../pub/System/ImagePlugin/style.css' media='all' />
+<base  /><!--[if IE]></base><![endif]--><link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
+<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
+<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
+<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
 <style type="text/css" media="all">
-@import url('../pub/System/SkinTemplates/base.css');
-</style>
-<style type="text/css" media="all">
-@import url('../pub/System/PatternSkinTheme2009/layout.css');
+@import url('../pub/System/PatternSkinTheme/layout.css');
 @import url('../pub/System/PatternSkinTheme2009/style.css');
 @import url('../pub/System/PatternSkinTheme2009/colors.css');
 </style>
-<style type="text/css" media="all">
-@import url('../pub/System/PatternSkinTheme2009/column_left.css');
-@import url('../pub/System/PatternSkinTheme2009/variant_twiki.css');
-</style><style type="text/css" media="all">
+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/column_left.css' media='all' type='text/css' />
+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/variant_twiki.css' media='all' type='text/css' /><style type="text/css" media="all">
 	/* Styles that are set using variables */
 	.patternBookView .foswikiTopRow,
-	.patternWebIndicator a img,
-	.patternWebIndicator a:hover img {
+	.patternWebIndicator,
+	.patternWebIndicator a {
 		background-color:#D0D0D0;
 	}
 	#patternTopBarContents { background-image:url(../pub/System/PatternSkin/header5.gif); background-repeat:repeat-x;}
@@ -50,14 +53,8 @@
 	
 
 
-<style type="text/css" media="all">
-	@import url("../pub/System/PatternSkin/print.css");
-</style>
-<!--[if IE]><style type="text/css" media="screen">
-pre {
-	height:1%;
-	overflow-x:auto;
-}
+<link rel='stylesheet' href='../pub/System/PatternSkin/print.css' media='all' type='text/css' />
+<!--[if IE 7 ]><style type="text/css" media="screen">
 .foswikiAttachments,
 .foswikiForm,
 .foswikiHelp,
@@ -79,7 +76,17 @@ pre {
 .foswikiFormStep {
 	height:100%;
 }
-#foswikiLogin,
+#foswikiLogin {
+	 margin-left: 25%;
+	 margin-right: 25%;
+}
+#foswikiLogin .foswikiFormSteps {
+	 width:auto;
+}
+#foswikiLogin input[type="text"],
+#foswikiLogin input[type="password"] {
+	 width: auto;
+}
 .patternShadow {
 	border:10px solid #fff;
 	margin-top:10px;
@@ -87,36 +94,33 @@ pre {
 	border:2px solid #ccc;
 }
 </style><![endif]-->
-<!--[if gt IE 8 ]><style type="text/css" media="screen">
-#foswikiLogin,
-.patternShadow {
-	border:10px solid #fff;
-	margin-top:10px;
-	margin-bottom:10px;
-	box-shadow: 0 0 10px #ccc;
-}
-</style><![endif]-->
-<link rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
-</head>
-<body class="foswikiNoJs patternViewPage">
-<a name="PageTop"></a><div class="foswikiPage"><div id="patternScreen">
+<!--[if lte IE 9]>
+
+<![endif]-->
+<!--[if gt IE 9]><!-->
+
+<!--<![endif]-->
+<!--JQUERYPLUGIN-->
+<!--JQUERYPLUGIN::MIGRATE-->
+<!--JQUERYPLUGIN::LIVEQUERY-->
+<!--JQUERYPLUGIN::FOSWIKI-->
+<!--JavascriptFiles/foswikiString-->
+<!--JavascriptFiles/foswikiForm-->
+<!--JQUERYPLUGIN::COMMENT-->
+<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
+<!--JavascriptFiles/foswikiPref-->
+<!--PatternSkin/pattern--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
+</head> 
+<body class="foswikiNoJs patternViewPage patternPrintPage">
+<span id="PageTop"></span><div class="foswikiPage"><div id="patternScreen">
 <div id="patternPageShadow">
 <div id="patternPage">
-<div id="patternWrapper"><div id="patternOuter">
+<div id="patternOuter" class="clear">
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-</div><div class="patternContent"><div class="foswikiTopic"><h1><a name="Quickstart_for_61_61WKM_61_61_users"></a>  Quickstart for <code><b>WKM</b></code> users </h1>
-<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
+<div id="patternMain">
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+<div class="patternContent"><div class="foswikiTopic"> <h1 id="Quickstart_for_61_61WKM_61_61_users">  Quickstart for <code><b>WKM</b></code> users </h1>
+<div class="foswikiToc" id="foswikiTOC"> <ul>
 <li> <a href="QuickStart.html#Quickstart_for_61_61WKM_61_61_users"> Quickstart for WKM users </a> <ul>
 <li> <a href="QuickStart.html#Introduction"> Introduction </a>
 </li> <li> <a href="QuickStart.html#Differences_between_61WKM_61_and_61musrfit_61_msr_files"> Differences between WKM and musrfit msr files </a>
@@ -124,16 +128,16 @@ pre {
 </li></ul> 
 </li></ul> 
 </div>
-<h2><a name="Introduction"></a>  Introduction </h2>
+<h2 id="Introduction">  Introduction </h2>
 <p></p>
-<code>musrfit</code> is a program suite for analyzing &mu;SR data. It is implemented in <code>C++/<a href="http://root.cern.ch/" target="_top">ROOT</a></code> and uses the <a href="http://www.cern.ch/minuit/" target="_top">MINUIT2</a> libraries developed at <a href="http://www.cern.ch/" target="_top">CERN</a> for fitting data.
+<code>musrfit</code> is a program suite for analyzing &mu;SR data. It is implemented in <code>C++/<a href="http://root.cern.ch/">ROOT</a></code> and uses the <a href="http://www.cern.ch/minuit/">MINUIT2</a> libraries developed at <a href="http://www.cern.ch/">CERN</a> for fitting data.
 Installation instructions for Linux, MS Windows, and Mac OS X can be found <a href="MusrFitSetup.html">here</a>. The full user manual is available <a href="MusrFit.html">here</a>.<br>
 In principle the programs can be used in the same fashion as <code>WKM</code> (<code>wkmfit, wkmview</code>).
 E.g., for fitting data as defined in the input file <code><b>8472.msr</b></code> one types:<pre>musrfit 8472.msr</pre> for plotting data and the corresponding 
 fit one calls:<pre>musrview 8472.msr</pre>
 Additionally, there are editors called <code><a href="MusrGui.html">musrgui/musredit</a></code> available which can do everything the <code>emacs</code> plug-in for <code>WKM</code> is capable of and even more. <strong><span class='foswikiRedFG'>However, before going to use only <code>musrgui</code> / <code>musredit</code> it is strongly recommended to read at least this "Quickstart" since there are a few differences between the programs as well as new features which are partially described in the following.</span></strong>
 <p></p>
-<h2><a name="Differences_between_61WKM_61_and_61musrfit_61_msr_files"></a>  Differences between <code>WKM</code> and <code>musrfit</code> msr files </h2>
+<h2 id="Differences_between_61WKM_61_and_61musrfit_61_msr_files">  Differences between <code>WKM</code> and <code>musrfit</code> msr files </h2>
 <p></p>
 The msr file format of <code>WKM</code> has some weaknesses and has therefore been extended for the use with <code>musrfit</code>. Existing <code>WKM</code> files can be converted using the <a href="MusrFit.html#Msr2Msr">small utility</a> <code>msr2msr</code>. The changes are: <ul>
 <li> The <code>musrfit</code> msr and mlog files contain an additional column in the FITPARAMETER block for the representation of positive uncertainties if <code>MINOS</code> was called during fitting. In that case the <strong>Step</strong> column holds the negative uncertainties. If there has not been performed an error analysis using <code>MINOS</code>, the symmetric error can be found in the <strong>Step</strong> column, whereas the <strong>Pos_Error</strong> column contains only <strong>none</strong> entries. The beginning of the FITPARAMETER block then might look like this <pre>
@@ -170,7 +174,7 @@ RUN 2008/lem08&#95;his&#95;8472 MUE4 PSI ROOT-NPP   (name beamline institute dat
 </li> <li> The commands <strong>SET BATCH</strong> and <strong>END RETURN</strong> may be omitted in the COMMANDS block.
 </li></ul> 
 <p></p>
-<h2><a name="Selected_new_features_in_61musrfit_61"></a>  Selected new features in <code>musrfit</code> </h2> <ul>
+<h2 id="Selected_new_features_in_61musrfit_61">  Selected new features in <code>musrfit</code> </h2> <ul>
 <li> If single-histogram fits are done, the normalization and background constants are given either "per nanosecond" or "per rebinned bin". The nanosecond normalization allows to change the binning without the need of re-doing the fit to the data.
 </li> <li> The use of functions in the RUN block is now possible for the normalization parameter, e.g. for the definition of an &alpha; parameter in simultaneous single-histogram fits of two histograms.
 </li> <li> Apart from the default &chi;<sup>2</sup> minimization, when doing single-histogram fits (fit type <strong>0</strong>) in <code>musrfit</code> there is also the possibility to do a log-likelihood maximization instead. For switching, just put <strong>MAX_LIKELIHOOD</strong> in the COMMANDS block.
@@ -200,7 +204,7 @@ RUN 2008/lem08&#95;his&#95;8472 MUE4 PSI ROOT-NPP   (name beamline institute dat
 <li> <strong>gamma_mu</strong> = &gamma;<sub>&mu;</sub>/2&pi; = 0.0135538817 MHz/G
 </li> <li> <strong>pi</strong> = &pi; = 3.14159265358979323846
 </li></ul> 
-</li> <li> As theory function also the so called skewed Gaussian can be chosen. The properties of this function are summarized in <a href="http://nemu.web.psi.ch/doc/LEM_Memo/skewedGaussian/skewedGaussian.pdf" target="_top">a memo</a> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/pdf.png" width="16" height="16" alt="pdf" /></span>. The function is called in the THEORY block as follows: <pre>
+</li> <li> As theory function also the so called skewed Gaussian can be chosen. The properties of this function are summarized in <a href="http://nemu.web.psi.ch/doc/LEM_Memo/skewedGaussian/skewedGaussian.pdf">a memo</a> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/pdf.png' width='16' height='16' alt='pdf' /></span>. The function is called in the THEORY block as follows: <pre>
    skewedGss   1  2  3  4 (phase frequency rate&#95;m rate&#95;p)
 </pre>
 </li> <li> After fitting it is possible to keep the <code>MINUIT2</code> output including the correlation matrix of the parameters. Calling <code>musrfit</code> with the <strong>--keep-mn2-ouput</strong> or <strong>-k</strong> option will provide you an ASCII and a ROOT file with the complete output, e.g. <pre>musrfit 8472.msr --keep-mn2-ouput</pre> generates <code><b>8472-mn2.output</b></code> and <code><b>8472-mn2.root</b></code> (and of course <code><b>8472.mlog</b></code>).
@@ -258,83 +262,29 @@ RUN 2008/lem08&#95;his&#95;8472 MUE4 PSI ROOT-NPP   (name beamline institute dat
 </pre> In the above example <code>musrfit</code> reads the data from the file <code><b>superconductor-data.db</b></code>; the <i>x</i> and <i>y</i> data are specified by the <strong>DB</strong> parameter names <code><b>range</b></code> and <code><b>field</b></code>. An alternative specification of the <i>x</i> and <i>y</i> data by the parameter number in the <strong>DB</strong> file is also possible!
 </li></ul> 
 <p></p>
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-@import url('../pub/System/PatternSkinTheme2009/layout.css');
+@import url('../pub/System/PatternSkinTheme/layout.css');
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+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/column_left.css' media='all' type='text/css' />
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-	height:1%;
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+<link rel='stylesheet' href='../pub/System/PatternSkin/print.css' media='all' type='text/css' />
+<!--[if IE 7 ]><style type="text/css" media="screen">
 .foswikiAttachments,
 .foswikiForm,
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@@ -79,7 +110,17 @@ pre {
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-</div><div class="patternContent"><div class="foswikiTopic"><h1><a name="A_61_61musrfit_61_61_Single_45Histogram_45Fit_Tutorial"></a>  <code><b>musrfit</b></code> Single-Histogram-Fit Tutorial </h1>
+<div id="patternMain">
+<div id="patternMainContents">
+<div class="patternContent"><div class="foswikiTopic"> <h1 id="A_61_61musrfit_61_61_Single_45Histogram_45Fit_Tutorial">  <code><b>musrfit</b></code> Single-Histogram-Fit Tutorial </h1>
 <p></p>
 The &mu;SR-data-analysis process using <code>musrfit</code> is based on so-called <code>msr</code> files. These files contain all information needed for the analysis such as names of the data files, a theory function, fit and plot parameters, and so on. It is the idea of this page to explain the basic use of an <code>msr</code> file and the different programs of the <code>musrfit</code> suite using the example of a single-histogram fit to time-differential transverse-field &mu;SR data. For a complete description of all options please refer to the <a href="MusrFit.html">manual</a>.
 <p></p>
-The example deals with a diamagnetic sample that has been measured in an applied field of approximately 150 G in the <a href="http://lmu.web.psi.ch/facilities/gps/gps.html" target="_top">GPS spectrometer</a> at <a href="http://www.psi.ch/" target="_top">PSI</a> using the "transverse geometry". In this geometry the muon spin is rotated about 50&#176; up and the field is applied parallel to the muon momentum. Hence, the relevant positron counters (to detect the spin precession) are placed above (histogram 3), below (histogram 4) and right of (histogram 5) the sample. The run numbers start from 3110.
+The example deals with a diamagnetic sample that has been measured in an applied field of approximately 150 G in the <a href="http://lmu.web.psi.ch/facilities/gps/gps.html">GPS spectrometer</a> at <a href="http://www.psi.ch/">PSI</a> using the "transverse geometry". In this geometry the muon spin is rotated about 50&#176; up and the field is applied parallel to the muon momentum. Hence, the relevant positron counters (to detect the spin precession) are placed above (histogram 3), below (histogram 4) and right of (histogram 5) the sample. The run numbers start from 3110.
 <p></p>
 To analyze these data (in a simple way) one starts out from the <code>msr</code> file <strong>3110_tutorial.msr</strong> provided together with the source-code distribution in the sub-directory <strong>doc/examples/</strong>. This ASCII file can be edited using any text editor. For convenience the editors <code>musredit</code>/<code>musrgui</code> are provided which offer some <code>msr</code>-file-specific functionalities and additionally serve as front ends to the underlying programs. In the following it is assumed that the file is open within <code>musredit</code>.
 <p></p>
-<h1><a name="A_1_The_61msr_61_file"></a> 1  The <code>msr</code> file </h1>
+<h1 id="A_1_The_61msr_61_file"> 1  The <code>msr</code> file </h1>
 <p></p>
 The <code>msr</code> file itself is divided into different blocks&mdash;a full description of the format can be found <a href="MusrFit.html#DescriptionOfTheMsrFileFormat">here</a>.
 In the file <strong>3110_tutorial.msr</strong> these blocks are successively: <ul>
@@ -230,134 +269,138 @@ STATISTIC --- 2011-07-09 10:58:44
 </pre> This block is the last block of a <code>msr</code> file. It contains some information on the fit: the date and time as well as the absolute and normalized values of &#967;<sup>2</sup> and the number of degrees of freedom in the fit.<br>   These information only have a meaning if the fitting procedure has been executed at least once and the fit has converged!
 </li></ul> 
 <p></p>
-<h1><a name="A_2_Determine_t0_and_the_data_range_using_61musrt0_61"></a> 2  Determine <i>t</i><sub>0</sub> and the data range using <code>musrt0</code> </h1>
+<h1 id="A_2_Determine_t0_and_the_data_range_using_61musrt0_61"> 2  Determine <i>t</i><sub>0</sub> and the data range using <code>musrt0</code> </h1>
 Before the given model can be fitted to the data, the data ranges and time zeros of the different RUN blocks have to be set correctly. This can be achieved using <code><a href="MusrFit.html#MusrT0">musrt0</a></code>. Starting this program by selecting the <img alt="musrt0.png" src="../pub/MUSR/MusrGui/musrt0.png" /> button in <code>musredit</code> or calling from a terminal <pre>musrt0 3110&#95;tutorial.msr</pre> opens an interactive window plotting the data of the first RUN block:<br />
-<img src="../pub/MUSR/TutorialSingleHisto/musrt0-1.png" alt="musrt0-1" align="center" /><br />
+<img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/musrt0-1.png' alt='musrt0-1' title='musrt0-1.png' width='708' height='529'   style='' /><br />
 The green line (at bin 1) represents time zero, the blue lines the start (at bin 1) and end (at bin 8000) of the data range and the optional red lines give the limits of the background range (if the background shall not be determined by the fit). All lines can be either dragged to reasonable locations or set by pressing the corresponding keyboard shortcuts. In the example the time zero can be set by pressing <strong>T</strong> (which moves the green line to the bin containing the maximum number of counts), the start of the data range should be set to about five bins later by zooming into the graph around bin 250 and pressing <strong>d</strong> when the cursor is found at a suitable location:<br />
-<img src="../pub/MUSR/TutorialSingleHisto/musrt0-2.png" alt="musrt0-2" width='708' height='529' align="center" /><br />
+<img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/igp_9c0f9b31d4414f37be0d3d171836fe63_musrt0-2.png' alt='musrt0-2' title='musrt0-2.png' width='688' height='529'   style='' /><br />
 After all lines have been adjusted for the first histogram, one can go on to the second by pressing <strong>q</strong>. This procedure is repeated until all ranges have been set correctly. When finished with the last histogram the new <i>t</i><sub>0</sub> and data-range values will be written to the <code>msr</code> file.
 A full description of <code>musrt0</code> can be found <a href="MusrFit.html#MusrT0">here</a>.
 <p></p>
-<h1><a name="A_3_Fit_the_model_to_the_data_using_61musrfit_61"></a> 3  Fit the model to the data using <code>musrfit</code> </h1>
+<h1 id="A_3_Fit_the_model_to_the_data_using_61musrfit_61"> 3  Fit the model to the data using <code>musrfit</code> </h1>
 Now that the basics of the <code>msr</code> file have been introduced and the necessary adjustments have been done one can proceed with fitting the specified model to the data. This is done by selecting the <img alt="musrfit.png" src="../pub/MUSR/MusrGui/musrfit.png" /> button in <code>musredit</code> or calling from a terminal <pre>musrfit 3110&#95;tutorial.msr</pre>
 <p></p>
 After the fitting procedure has finished the <code>msr</code> file is updated and contains the newly determined values of the fit parameters.
 <p></p>
-<h1><a name="A_4_View_the_data_and_the_fit_using_61musrview_61"></a> 4  View the data and the fit using <code>musrview</code> </h1>
+<h1 id="A_4_View_the_data_and_the_fit_using_61musrview_61"> 4  View the data and the fit using <code>musrview</code> </h1>
 The data and the corresponding fit can be visualized by choosing <img alt="musrview.png" src="../pub/MUSR/MusrGui/musrview.png" /> in <code>musredit</code> or calling from a terminal <pre>musrview 3110&#95;tutorial.msr</pre> This creates the windows according to the given PLOT blocks in the <code>msr</code> file:<br />
-<img src="../pub/MUSR/TutorialSingleHisto/musrview-1.png" alt="musrview-1" align="center" /><br />
-<img src="../pub/MUSR/TutorialSingleHisto/musrview-2.png" alt="musrview-2" align="center" /><br />
+<img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/musrview-1.png' alt='musrview-1' title='musrview-1.png' width='808' height='629'   style='' /><br />
+<img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/musrview-2.png' alt='musrview-2' title='musrview-2.png' width='808' height='629'   style='' /><br />
 The basic features of <code>musrview</code> can be found in the Musrfit menu. They include: <ul>
 <li> export the shown data and the model to an ASCII file with comma-separated values   
 </li> <li> presenting the difference between the shown data and the model (keyboard shortcut: <strong>d</strong>)
-</li> <li> calculate and show the Fourier transform of the shown data (keyboard shortcut: <strong>f</strong>), e.g. for the asymmetry of the "Up" and "Down" detectors:<br />   <img src="../pub/MUSR/TutorialSingleHisto/musrview-3.png" alt="musrview-3" align="center" /><br />
+</li> <li> calculate and show the Fourier transform of the shown data (keyboard shortcut: <strong>f</strong>), e.g. for the asymmetry of the "Up" and "Down" detectors:<br />   <img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/musrview-3.png' alt='musrview-3' title='musrview-3.png' width='808' height='629'   style='' /><br />
 </li></ul> 
 <p></p>
-<h1><a name="A_5_Process_multiple_61msr_61_files_using_61msr2data_61"></a> 5  Process multiple <code>msr</code> files using <code>msr2data</code> </h1>
+<h1 id="A_5_Process_multiple_61msr_61_files_using_61msr2data_61"> 5  Process multiple <code>msr</code> files using <code>msr2data</code> </h1>
 This short introduction is concluded by calling attention to the program <code><a href="Msr2Data.html">msr2data</a></code>. As the name indicates the main purpose of this program is to extract the FITPARAMETER-block information from multiple <code>msr</code> files with the same structure and to summarize them in a single ASCII file (either in TRIUMF DB format or simple columns). However, as described in detail in the <code><a href="Msr2Data.html">manual</a></code>, it is not only possible to collect data from <code>msr</code> files but also to create new <code>msr</code> files from a template and to process these files using <code>musrfit</code> on the fly.<br>
 Assuming the successive runs <strong>3111</strong> through <strong>3114</strong> can be analyzed using the same model introduced above for run <strong>3110</strong> (e.g. in the case one has done measurements at different temperatures) one can use the file <strong>3110_tutorial.msr</strong> as template, generate the files <strong>3111_tutorial.msr</strong> through <strong>3114_tutorial.msr</strong> with the corresponding updates in the RUN blocks, call for each one <code>musrfit</code> and finally summarize the FITPARAMETER-block information of all processed files in an ASCII output file <strong>tutorial-T-dependence.dat</strong> (simple columns). If further information on the temperature or the applied field is available in the data files these will be included as well in the resulting ASCII file.<br>
 From the terminal this would be done as follows:<pre>
 msr2data 3110 3114 &#95;tutorial fit-3110 -o tutorial-T-dependence.dat data
 </pre>
 To achieve the same in <code>musredit</code> one selects <img alt="musrmsr2data.png" src="../pub/MUSR/MusrGui/musrmsr2data.png" /> and fills the form accordingly:<br />
-<img src="../pub/MUSR/TutorialSingleHisto/msr2data.png" alt="msr2data" align="center" />
+<img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/msr2data.png' alt='msr2data' title='msr2data.png' width='612' height='605'   style='' />
 <p></p>
-<h1><a name="A_6_Further_reading"></a> 6  Further reading </h1>
+<h1 id="A_6_Further_reading"> 6  Further reading </h1>
 This page only summarizes the very basic features and options of the programs contained in the <code>musrfit</code> suite. For a complete description please refer to the manuals of <ul>
 <li> <code><a href="MusrFit.html">musrfit</a></code> (including <code><a href="MusrFit.html#MusrFit">musrfit</a></code>, <code><a href="MusrFit.html#MusrView">musrview</a></code>, <code><a href="MusrFit.html#MusrT0">musrt0</a></code> and the full description of the <a href="MusrFit.html#DescriptionOfTheMsrFileFormat"><code>msr</code>-file format</a>)
 </li> <li> <code><a href="MusrGui.html">musredit</a></code>
 </li> <li> <code><a href="Msr2Data.html">msr2data</a></code>.
 </li></ul> 
 <p></p>
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-<ul><li class="patternLogIn"><a href="https://intranet.psi.ch/wiki/bin/logon/MUSR/TutorialSingleHisto">Log In</a> or <a href="https://intranet.psi.ch/System/UserRegistration">Register</a></li></ul>
-</div>
+-- <a href="http://www.fsf.org/register_form?referrer=8369">BMW</a> &amp; <a href="http://lmu.web.psi.ch/lem/group.html">AS</a> </div>
 <p></p>
 <p></p>
-<b>PSI Webs</b> <ul>
-<li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/psi.png" width="16" height="16" alt="psi" /></span> <a href="https://intranet.psi.ch/Main/WebHome">Main</a>
-</li> <li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/psi.png" width="16" height="16" alt="psi" /></span> <a href="https://intranet.psi.ch/Main/WebList">weitere Webs</a>
-</li></ul> 
-<hr />
-<b>System Webs</b> <ul>
-<li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/foswiki.png" width="16" height="16" alt="foswiki" /></span> <a href="https://intranet.psi.ch/Sandbox/WebHome">Sandbox</a>
-</li> <li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/foswiki.png" width="16" height="16" alt="foswiki" /></span> <a href="https://intranet.psi.ch/System/WebHome">Documentation</a>
-</li></ul> 
-<hr /> <ul>
-<li> <a href="https://intranet.psi.ch/MUSR/WebCreateNewTopic?parent=TutorialSingleHisto" target="_top"><span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/newtopic.png" width="16" height="16" alt="newtopic" /></span> Create New Topic</a> 
-</li> <li> <a href="WebTopicList.html"> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/index.png" width="16" height="16" alt="index" /></span> Show All Topics</a> 
-</li> <li> <a href="WebSearch.html"> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/searchtopic.png" width="16" height="16" alt="searchtopic" /></span> Search in Topics</a> 
-</li> <li> <a href="WebChanges.html"> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/changes.png" width="16" height="16" alt="changes" /></span> Recent Changes</a>
-</li> <li> <a href="WebNotify.html"> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/notify.png" width="16" height="16" alt="notify" /></span> Define Notifications</a>
-</li></ul> 
-<p></p>
-</div></div>
-</div>
-<div class="clear">&nbsp;</div>
-</div></div><div id="patternTopBar">
-<div id="patternTopBarContentsWrapper">
-<div id="patternTopBarContents"><table border="0" cellpadding="0" cellspacing="0" style="width:100%" summary="">
-<tr><td valign="middle"><span id="foswikiLogo" class="foswikiImage"><a href="WebHome.html"><img src="../pub/Main/WebPreferences/psi_logo_150.gif" border="0" alt="Paul Scherrer Institut" style="border:none; margin: -8px 0 0 15px;" /></a></span></td>
-<td align="right" valign="top" class="patternMetaMenu" id="psimetanav">
-<p></p> <ul>
-<li> <form name="quickSearchForm" id="solrSearchForm" action="https://intranet.psi.ch/PSI/Search"><input type="hidden" name="filter" value="web:MUSR" /><input type="text" class="foswikiInputField" id="quickSearchBox" name="search" value="" size="18" /><input type="hidden" name="scope" value="all" /><!-- <input type="hidden" name="web" value="MUSR" /> --> <noscript>&nbsp;<input type="submit" size="5" class="foswikiButton" name="submit" value="Search" />&nbsp;</noscript><input type="image" class="searchsubmit" alt="Search" value="Suche..." name="sa" src="../webbase/img/search.png">	</form>
-</li> <li> <form name="changeLanguage"    action="https://intranet.psi.ch/wiki/bin/oops/MUSR/TutorialSingleHisto" method="get">    <input type="hidden" name="redirectto" value="/MUSR/TutorialSingleHisto?cover=print" />    <select name="language" class="foswikiSelect"        onchange="document.changeLanguage.submit()">    <option  value="de">Deutsch</option> <option selected="selected" value="en">English</option></select>    <input type="hidden" name="template" value="oopslanguagechanged" />    <noscript>        <input class="foswikiButton" type="submit"            value="Change language" />    </noscript> </form>
-</li></ul> 
-<p></p>
-<p></p>
-<p></p>
-</td></tr></table>
-</div><!--/patternTopBarContents-->
-</div><!--/patternTopBarContentsWrapper-->
-</div><!-- /patternTopBar--><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar">Ideas, requests, problems regarding <a href="https://intranet.psi.ch/Main/WebHome">PSI Wiki</a>? <a href="mailto&#58;psi&#46;intranet&#64;psi&#46;ch&#63;subject&#61;PSI&#32;Wiki&#37;20Feedback&#37;20on&#37;20MUSR&#46;TutorialSingleHisto">Send feedback</a></div></div></div>
+<br class="imageClear" clear="all"/><div class="foswikiAttachments">
+<div class="twistyPlugin foswikiMakeVisible"><span id="topicattachmentslist1show" style="display:none" class="twistyRememberSetting twistyTrigger foswikiUnvisited twistyInited"><a class="patternTwistyButton" href="#"><img src="../pub/System/DocumentGraphics/toggleopen.png" border="0" alt="" /><span class="foswikiLinkLabel foswikiUnvisited">Attachments <span class='foswikiSmall foswikiGrayText'>6</span></span></a></span><span id="topicattachmentslist1hide" style="display:none" class="twistyRememberSetting twistyTrigger foswikiUnvisited twistyInited"><a class="patternTwistyButton" href="#"><img src="../pub/System/DocumentGraphics/toggleclose.png" border="0" alt="" /><span class="foswikiLinkLabel foswikiUnvisited">Attachments <span class='foswikiSmall foswikiGrayText'>6</span></span></a></span></div><div class="twistyPlugin"><div id="topicattachmentslist1toggle" style="" class="twistyRememberSetting twistyContent twistyInited">
+<table border="1" class="foswikiTable" id="tableTutorialSingleHisto1" rules="none" summary="Topic attachments"><caption>Topic attachments</caption>
+	<thead>
+		<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<th class="foswikiTableCol0 foswikiFirstCol"> <a href="https://intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print;sortcol=0;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">I</a> </th>
+			<th class="foswikiTableCol1"> <a href="https://intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print;sortcol=1;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Attachment</a> </th>
+			<th class="foswikiTableCol2"> <a href="https://intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print;sortcol=2;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Action</a> </th>
+			<th class="foswikiTableCol3"> <a href="https://intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print;sortcol=3;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Size</a> </th>
+			<th class="foswikiTableCol4"> <a href="https://intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print;sortcol=4;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Date</a> </th>
+			<th class="foswikiTableCol5"> <a href="https://intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print;sortcol=5;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Who</a> </th>
+			<th class="foswikiTableCol6 foswikiLastCol"> <a href="https://intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print;sortcol=6;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Comment</a> </th>
+		</tr>
+	</thead>
+	<tbody>
+		<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<td class="foswikiTableCol0 foswikiFirstCol"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='msr2data.png' /></span><span class="foswikiHidden">png</span> </td>
+			<td class="foswikiTableCol1"> <a href="../pub/MUSR/TutorialSingleHisto/msr2data.png">msr2data.png</a> </td>
+			<td class="foswikiTableCol2"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/TutorialSingleHisto?filename=msr2data.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
+			<td class="foswikiTableCol3" style="text-align:right"> 34 K </td>
+			<td class="foswikiTableCol4"> <span class="foswikiNoBreak">20 Jul 2011 - 13:34</span> </td>
+			<td class="foswikiTableCol5"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
+			<td class="foswikiTableCol6 foswikiLastCol"> &nbsp; </td>
+		</tr>
+		<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<td class="foswikiTableCol0 foswikiFirstCol"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='musrt0-1.png' /></span><span class="foswikiHidden">png</span> </td>
+			<td class="foswikiTableCol1"> <a href="../pub/MUSR/TutorialSingleHisto/musrt0-1.png">musrt0-1.png</a> </td>
+			<td class="foswikiTableCol2"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/TutorialSingleHisto?filename=musrt0-1.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
+			<td class="foswikiTableCol3" style="text-align:right"> 19 K </td>
+			<td class="foswikiTableCol4"> <span class="foswikiNoBreak">20 Jul 2011 - 13:38</span> </td>
+			<td class="foswikiTableCol5"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
+			<td class="foswikiTableCol6 foswikiLastCol"> &nbsp; </td>
+		</tr>
+		<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<td class="foswikiTableCol0 foswikiFirstCol"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='musrt0-2.png' /></span><span class="foswikiHidden">png</span> </td>
+			<td class="foswikiTableCol1"> <a href="../pub/MUSR/TutorialSingleHisto/musrt0-2.png">musrt0-2.png</a> </td>
+			<td class="foswikiTableCol2"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/TutorialSingleHisto?filename=musrt0-2.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
+			<td class="foswikiTableCol3" style="text-align:right"> 19 K </td>
+			<td class="foswikiTableCol4"> <span class="foswikiNoBreak">09 Jul 2011 - 15:17</span> </td>
+			<td class="foswikiTableCol5"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
+			<td class="foswikiTableCol6 foswikiLastCol"> &nbsp; </td>
+		</tr>
+		<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<td class="foswikiTableCol0 foswikiFirstCol"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='musrview-1.png' /></span><span class="foswikiHidden">png</span> </td>
+			<td class="foswikiTableCol1"> <a href="../pub/MUSR/TutorialSingleHisto/musrview-1.png">musrview-1.png</a> </td>
+			<td class="foswikiTableCol2"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/TutorialSingleHisto?filename=musrview-1.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
+			<td class="foswikiTableCol3" style="text-align:right"> 45 K </td>
+			<td class="foswikiTableCol4"> <span class="foswikiNoBreak">09 Jul 2011 - 15:48</span> </td>
+			<td class="foswikiTableCol5"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
+			<td class="foswikiTableCol6 foswikiLastCol"> &nbsp; </td>
+		</tr>
+		<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<td class="foswikiTableCol0 foswikiFirstCol"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='musrview-2.png' /></span><span class="foswikiHidden">png</span> </td>
+			<td class="foswikiTableCol1"> <a href="../pub/MUSR/TutorialSingleHisto/musrview-2.png">musrview-2.png</a> </td>
+			<td class="foswikiTableCol2"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/TutorialSingleHisto?filename=musrview-2.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
+			<td class="foswikiTableCol3" style="text-align:right"> 36 K </td>
+			<td class="foswikiTableCol4"> <span class="foswikiNoBreak">09 Jul 2011 - 15:48</span> </td>
+			<td class="foswikiTableCol5"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
+			<td class="foswikiTableCol6 foswikiLastCol"> &nbsp; </td>
+		</tr>
+		<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='musrview-3.png' /></span><span class="foswikiHidden">png</span> </td>
+			<td class="foswikiTableCol1 foswikiLast"> <a href="../pub/MUSR/TutorialSingleHisto/musrview-3.png">musrview-3.png</a> </td>
+			<td class="foswikiTableCol2 foswikiLast"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/TutorialSingleHisto?filename=musrview-3.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
+			<td class="foswikiTableCol3 foswikiLast" style="text-align:right"> 42 K </td>
+			<td class="foswikiTableCol4 foswikiLast"> <span class="foswikiNoBreak">09 Jul 2011 - 16:01</span> </td>
+			<td class="foswikiTableCol5 foswikiLast"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
+			<td class="foswikiTableCol6 foswikiLastCol foswikiLast"> &nbsp; </td>
+		</tr>
+	</tbody></table>
+</div></div></div></div>
+<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>TutorialSingleHisto <br />
+Topic revision:  <span class='patternRevInfo'>02 Sep 2011, wojek</span></div>
 </div>
 </div>
 </div>
-</div></body>
-<!-- Mirrored from intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 18 Dec 2014 13:46:03 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=iso-8859-1"><!-- /Added by HTTrack -->
-</html>
+</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar"><span class="foswikiRight"> <a href="http://foswiki.org/"><img src="../pub/System/ProjectLogos/foswiki-badge.png" alt="This site is powered by Foswiki" title="This site is powered by Foswiki" /></a></span>Copyright &copy; by the contributing authors. All material on this collaboration platform is the property of the contributing authors. <br /> Ideas, requests, problems regarding PSI Wiki? <a href='mailto:thomas.buecklers@psi.ch?subject=PSI Wiki %20Feedback%20on%20MUSR.TutorialSingleHisto'>Send feedback</a></div></div></div>
+</div>
+</div>
+</div>
+</div></div><!-- /endWrap -->
 <p></p>
-<p></p>
-<p></p>
-<p></p>
+<!-- Piwik -->
+
+<noscript><p><img src="../piwik/piwikf832.gif?idsite=7" style="border:0" alt=""></p></noscript>
+<!-- End Piwik Tag -->
+
+
+</body>
+
+<!-- Mirrored from intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:00:58 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+</html>

doc/html/user/MUSR/WebHome.html

@@ -1,35 +1,38 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en_US" lang="en_US">
+<!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/WebHome?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 18 Dec 2014 13:46:47 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=iso-8859-1"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/WebHome?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:33 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
 <head>
 <link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
-<title>   MUSR :: MUSR</title>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+<title> MUSR :: MUSR</title>
+<meta http-equiv="X-UA-Compatible" content="IE=edge" />
+<meta charset="utf-8" />
+<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1.5, user-scalable=yes" />
+<meta name="mobile-web-app-capable" content="yes" />
+<meta name="mobile-web-app-status-bar-style" content="black-translucent" />
+<meta name="apple-mobile-web-app-capable" content="yes" />
+<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
 <link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
 <link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/WebHome?t=1418910337" type="application/x-wiki" title="edit WebHome" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/WebHome?t=1481904045" type="application/x-wiki" title="edit WebHome" />
 <meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
 <meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
 <meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
-<base  /><!--[if IE]></base><![endif]-->
-<link rel='stylesheet' href='../pub/System/ImagePlugin/style.css' media='all' />
+<base  /><!--[if IE]></base><![endif]--><link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
+<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
+<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
+<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
 <style type="text/css" media="all">
-@import url('../pub/System/SkinTemplates/base.css');
-</style>
-<style type="text/css" media="all">
-@import url('../pub/System/PatternSkinTheme2009/layout.css');
+@import url('../pub/System/PatternSkinTheme/layout.css');
 @import url('../pub/System/PatternSkinTheme2009/style.css');
 @import url('../pub/System/PatternSkinTheme2009/colors.css');
 </style>
-<style type="text/css" media="all">
-@import url('../pub/System/PatternSkinTheme2009/column_left.css');
-@import url('../pub/System/PatternSkinTheme2009/variant_twiki.css');
-</style><style type="text/css" media="all">
+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/column_left.css' media='all' type='text/css' />
+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/variant_twiki.css' media='all' type='text/css' /><style type="text/css" media="all">
 	/* Styles that are set using variables */
 	.patternBookView .foswikiTopRow,
-	.patternWebIndicator a img,
-	.patternWebIndicator a:hover img {
+	.patternWebIndicator,
+	.patternWebIndicator a {
 		background-color:#D0D0D0;
 	}
 	#patternTopBarContents { background-image:url(../pub/System/PatternSkin/header5.gif); background-repeat:repeat-x;}
@@ -50,14 +53,8 @@
 	
 
 
-<style type="text/css" media="all">
-	@import url("../pub/System/PatternSkin/print.css");
-</style>
-<!--[if IE]><style type="text/css" media="screen">
-pre {
-	height:1%;
-	overflow-x:auto;
-}
+<link rel='stylesheet' href='../pub/System/PatternSkin/print.css' media='all' type='text/css' />
+<!--[if IE 7 ]><style type="text/css" media="screen">
 .foswikiAttachments,
 .foswikiForm,
 .foswikiHelp,
@@ -79,7 +76,17 @@ pre {
 .foswikiFormStep {
 	height:100%;
 }
-#foswikiLogin,
+#foswikiLogin {
+	 margin-left: 25%;
+	 margin-right: 25%;
+}
+#foswikiLogin .foswikiFormSteps {
+	 width:auto;
+}
+#foswikiLogin input[type="text"],
+#foswikiLogin input[type="password"] {
+	 width: auto;
+}
 .patternShadow {
 	border:10px solid #fff;
 	margin-top:10px;
@@ -87,38 +94,35 @@ pre {
 	border:2px solid #ccc;
 }
 </style><![endif]-->
-<!--[if gt IE 8 ]><style type="text/css" media="screen">
-#foswikiLogin,
-.patternShadow {
-	border:10px solid #fff;
-	margin-top:10px;
-	margin-bottom:10px;
-	box-shadow: 0 0 10px #ccc;
-}
-</style><![endif]-->
-<link rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
-</head>
-<body class="foswikiNoJs patternViewPage">
-<a name="PageTop"></a><div class="foswikiPage"><div id="patternScreen">
+<!--[if lte IE 9]>
+
+<![endif]-->
+<!--[if gt IE 9]><!-->
+
+<!--<![endif]-->
+<!--JQUERYPLUGIN-->
+<!--JQUERYPLUGIN::MIGRATE-->
+<!--JQUERYPLUGIN::LIVEQUERY-->
+<!--JQUERYPLUGIN::FOSWIKI-->
+<!--JavascriptFiles/foswikiString-->
+<!--JavascriptFiles/foswikiPref-->
+<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
+<!--JQUERYPLUGIN::COMMENT-->
+<!--JavascriptFiles/foswikiForm-->
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+<div id="patternMain">
+<div id="patternMainContents">
+<div class="patternContent"><div class="foswikiTopic"> <h1 id="Welcome_to_the_MUSR_web">  Welcome to the MUSR web </h1>
 <p></p>
-<p></p>
-      	
-      	
-      	
-<p></p>
-<p></p>
-<p></p>
-<p></p>
-</div><div class="patternContent"><div class="foswikiTopic"><h1><a name="Welcome_to_the_MUSR_web"></a>  Welcome to the MUSR web </h1>
-<p></p>
-<h2><a name="Documentation_of_the_SR_data_analysis_suite_61musrfit_61"></a>  Documentation of the &#956;SR data analysis suite <code>musrfit</code> </h2> <ul>
-<li> <a href="CiteMusrFit.html">How to cite <code>musrfit</code>? <img src="../pub/Main/SmiliesPluginPSI/yes.gif" alt="yes" title="yes" border="0" /> </a>
+<h2 id="Documentation_of_the_SR_data_analysis_suite_61musrfit_61">  Documentation of the &#956;SR data analysis suite <code>musrfit</code> </h2> <ul>
+<li> <a href="CiteMusrFit.html">How to cite <code>musrfit</code>? <img class='smily' src='../pub/Main/SmiliesPluginPSI_/yes.gif' alt='yes' title='yes' /> </a>
 </li> <li> <a href="TutorialSingleHisto.html">Single-histogram-fit tutorial for <code>musrfit</code> introducing the basic features of the programs and <code>msr</code> files</a> 
 </li> <li> <a href="MusrFit.html">User manual of the &#956;SR data analysis software <code>musrfit</code> </a>
 </li> <li> <a href="MusrFitSetup.html">Setting up <code>musrfit</code> on Different Platforms</a>
@@ -126,7 +130,7 @@ pre {
 </li> <li> <a href="MusrGui.html">Documentation of <code>musrgui</code>/<code>musredit</code>&mdash;editors interfacing <code>musrfit</code> </a>
 </li> <li> <a href="Msr2Data.html">Documentation of <code>msr2data</code>&mdash;a program for automatically processing multiple musrfit <code>msr</code> files</a>
 </li> <li> <a href="MusrFit.html#Any2Many"><code>any2many</code>&mdash;a universal &#956;SR-file-format converter</a> 
-</li> <li> <a href="MusrRoot.html"><code>MusrRoot</code>: an extensible open file format for &#956;SR</a> <img src="../pub/System/DocumentGraphics/new.png" width="30" height="16" alt="New" border="0" /> 
+</li> <li> <a href="MusrRoot.html"><code>MusrRoot</code>: an extensible open file format for &#956;SR</a>
 </li> <li> Documentation of user libs (user functions) <ul>
 <li> <a href="BmwLibs.html">Meissner-Profiles / Vortex-Lattice related functions (BMW libs)</a>
 </li> <li> Nonlocal superconductivity related Meissner screening functions (AS libs)
@@ -134,83 +138,29 @@ pre {
 </li> <li> <a href="MusrFitAcknowledgements.html">Acknowledgements</a>
 </li></ul> 
 <p></p>
---  <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a> &amp; (<a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a>) - last update Dec 18, 2014 </div>
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+--  <a href="http://www.psi.ch/low-energy-muons/people">AS</a> &amp; (<a href="http://www.fsf.org/register_form?referrer=8369">BMW</a>) - last update Dec 15, 2016</div>
+<p></p>
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+Topic revision:  <span class='patternRevInfo'>15 Dec 2016, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
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doc/html/user/pub/MUSR/MusrFit/Makefile.html

@@ -0,0 +1,60 @@
+#---------------------------------------------------
+# get compilation flags from root-config
+
+ROOTCFLAGS    = $(shell $(ROOTSYS)/bin/root-config --cflags)
+
+#---------------------------------------------------
+
+OS            = LINUX
+CXX           = g++
+CXXFLAGS      = -O3 -Wall -Wno-trigraphs -fPIC
+LOCALINCLUDE  = .
+ROOTINCLUDE   = $(ROOTSYS)/include
+INCLUDES      = -I$(LOCALINCLUDE) -I$(ROOTINCLUDE)
+LD            = g++
+LDFLAGS       =
+SOFLAGS       = -O -shared
+
+# the output from the root-config script:
+CXXFLAGS      += $(ROOTCFLAGS)
+LDFLAGS       +=
+
+# some definitions: headers (used to generate *Dict* stuff), sources, objects,...
+OBJS =
+OBJS += TMyFunction.o TMyLibraryDict.o
+
+SHLIB = libTMyLibrary.so
+
+# make the shared lib:
+#
+all:  $(SHLIB)
+
+$(SHLIB): $(OBJS)
+	@echo "---> Building shared library $(SHLIB) ..."
+	/bin/rm -f $(SHLIB)
+	$(LD) $(OBJS) $(SOFLAGS) -o $(SHLIB)
+	@echo "done"
+
+# clean up: remove all object file (and core files)
+# semicolon needed to tell make there is no source
+# for this target!
+#
+clean:; 	@rm -f $(OBJS) *Dict* core*
+	@echo "---> removing $(OBJS)"
+
+#
+$(OBJS): %.o: %.cpp
+	$(CXX) $(INCLUDES) $(CXXFLAGS) -c $<
+
+# Generate the ROOT CINT dictionary
+
+TMyLibraryDict.cpp: TMyFunction.h TMyLibraryLinkDef.h
+	@echo "Generating dictionary $@..."
+	rootcint -f $@ -c -p -I$(ROOTINCLUDE) $^
+
+install: all
+	@echo "Installing shared lib: libTApproximation.so"
+ifeq ($(OS),LINUX)
+	cp -pv $(SHLIB) $(ROOTSYS)/lib
+	cp -pv $(LOCALINCLUDE)/*.h $(ROOTSYS)/include
+endif

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doc/html/user/pub/System/PatternSkinTheme2009/column_left.css

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-*/
-
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-#patternSideBar {
-	width:16em;
-	margin-left:-16em;
-}
+#patternOuter{margin-left:16em}#patternSideBar{width:16em;margin-left:-16em}

doc/html/user/pub/System/PatternSkinTheme2009/variant_twiki.css

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doc/html/user/pub/System/PsiSkin/psistyle.css

@@ -99,7 +99,8 @@ blockquote.psi {
 
 /* DMS Icon */
 
-.patternContent a[href^="http:"] {
+.patternContent a[href^="http:"],
+.patternContent a[href^="https:"] {
    background-image: url(../DocumentGraphics/external.gif);
    background-position:  right center;
    background-repeat:  no-repeat;
@@ -107,11 +108,14 @@ blockquote.psi {
 }
 
 .patternContent a[href^="http:"]:hover, 
-.patternContent a[href^="http:"]:visited:hover {
+.patternContent a[href^="http:"]:visited:hover,
+.patternContent a[href^="https:"]:hover, 
+.patternContent a[href^="https:"]:visited:hover {
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-.patternContent a[href^="http:"]:visited {
+.patternContent a[href^="http:"]:visited,
+.patternContent a[href^="https:"]:visited {
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@@ -128,14 +132,17 @@ blockquote.psi {
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-.patternContent a[href^="http://i.psi.ch"] {
+.patternContent a[href^="http://i.psi.ch"],
+.patternContent a[href^="https://intranet.psi.ch"] {
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-.patternContent a[href^="http://i.psi.ch"]:visited:hover {
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+.patternContent a[href^="https://intranet.psi.ch"]:hover,
+.patternContent a[href^="https://intranet.psi.ch"]:visited:hover {
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@@ -175,7 +182,7 @@ caption {
 
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 :lang(en)    { quotes:"\201C" "\201D" "\2018" "\2019"; }
-:lang(fr)    { quotes:"\00AB\A0" "\A0\00BB" "\2039\A0" "\A0\203A"; }
+:lang(fr)    { quotes:"\00AB" "\00BB" "\2039" "\203A"; }
 
 q:before { content:open-quote; color:#000000; }
 q:after { content:close-quote; color:#000000; }

doc/memos/rrf/rrf-notes.tex

@@ -0,0 +1,265 @@
+\documentclass[twoside]{article}
+
+\usepackage[english]{babel}
+\usepackage{a4}
+\usepackage{amssymb}
+\usepackage{graphicx}
+\usepackage{fancyhdr}
+\usepackage{array}
+\usepackage{float}
+\usepackage{hyperref}
+\usepackage{xspace}
+\usepackage{rotating}
+\usepackage{dcolumn}
+\usepackage{url}
+
+\setlength{\topmargin}{10mm}
+\setlength{\topmargin}{-13mm}
+% \setlength{\oddsidemargin}{0.5cm}
+% \setlength{\evensidemargin}{0cm}
+\setlength{\oddsidemargin}{1cm}
+\setlength{\evensidemargin}{1cm}
+\setlength{\textwidth}{14.5cm}
+\setlength{\textheight}{23.8cm}
+
+\def\mathbi#1{\textbf{\em #1}}
+
+\pagestyle{fancyplain}
+\addtolength{\headwidth}{0.6cm}
+\fancyhead{}%
+\fancyhead[RE,LO]{\bf RRF Fits}%
+\fancyhead[LE,RO]{\thepage}
+\cfoot{--- Andreas Suter -- \today ---}
+\rfoot{\includegraphics[width=6.4cm]{PSI_Logo_wide_blau.pdf}}
+
+\DeclareMathAlphabet{\bi}{OML}{cmm}{b}{it}
+
+\newcommand{\mean}[1]{\langle #1 \rangle}
+\newcommand{\lem}{LE-$\mu$SR\xspace}
+\newcommand{\musr}{$\mu$SR\xspace}
+\newcommand{\etal}{\emph{et al.\xspace}}
+\newcommand{\ie}{\emph{i.e.\xspace}}
+\newcommand{\eg}{\emph{e.g.\xspace}}
+
+\newcolumntype{d}[1]{D{.}{.}{#1}}
+
+\begin{document}
+
+% Header info --------------------------------------------------
+\thispagestyle{empty}
+\noindent
+\begin{tabular}{@{\hspace{-0.7cm}}l@{\hspace{6cm}}r}
+\noindent\includegraphics[width=3.4cm]{PSI_Logo_narrow_blau.jpg} &
+  {\Huge\sf Memorandum}
+\end{tabular}
+%
+\vskip 1cm
+%
+\begin{tabular}{@{\hspace{-0.5cm}}ll@{\hspace{4cm}}ll}
+Datum:   & \today        &     & \\[3ex]
+Von:     & Andreas Suter & An: & \\
+Telefon: & +41\, (0)56\, 310\, 4238        &     & \\
+Raum:    & WLGA / 119    & cc: & \\
+e-mail:  & \verb?andreas.suter@psi.ch? & & \\
+\end{tabular}
+%
+\vskip 0.3cm
+\noindent\hrulefill
+\vskip 1cm
+%
+\section{Rotating Reference Frame Fits}
+
+High transverse field \musr (HTF-\musr) experiments will typically lead to
+rather large data sets since it is necessary to follow the high frequencies
+present in the positron decay histograms. Currently the HAL-9500 instrument 
+at PSI \cite{HAL9500} is operated with $2\time 8$ positron detector, with a 
+typical number of $\sim 4\times 10^5$ histogram bins. To analyze HTF-\musr 
+data on rather slugish computer hardware is a challenge. In the last millennium
+the people invented the rotating reference frame transformation (RRF) \cite{Riseman90}
+to reduce to data sets to be handled.
+
+Here I will shortly describe the ways how it is implemented in \textsc{Musrfit},
+and why it should be avoided to be used altogether. The starting point of all
+is given by the positron decay spectrum which formally takes the form
+
+\begin{equation}\label{eq:positron_decay_spectrum}
+ N^{(j)}(t) = N_0^{(j)} \exp(-t / \tau_\mu) \, \left[ 1 + A^{(j)}(t) \right] + N_{\rm bkg}^{(j)},
+\end{equation}
+
+\noindent where $(j)$ is the index of the positron counter, $N_0$ gives the scale
+of recorded positrons, $\tau_\mu$ is the muon lifetime, $A(t)$ the asymmetry, and $N_{\rm bkg}$
+describes the background due to uncorrelated events.
+
+The idea behind the RRF is twofolded: (i) try to extract $A(t)$, and (ii) shift the high frequency
+data set $A(t)$ to lower frequencies such that the number of necessary bins needed can be
+reduced (packing / rebinning), and hence the overall number of bins is much smaller.
+
+As I will try to explain, this is not for free, and there are problems arising from
+this kind of data treatment.
+
+\subsection{Single Histogram RRF Implementation}
+
+In a first step the asymmetry needs to be determined. This is done the following way:
+\begin{enumerate}
+ \item Determine the background, $N_{\rm bkg}$, at times before $t_0$ ($t_0$ is the time of the muon
+       implantation). Hopefully the background before and after $t_0$ is equal, which is not always
+       the case.
+ \item Multiple the background corrected histogram with $\exp(+t / \tau_\mu)$, this is leading to
+\end{enumerate}
+
+\begin{equation}\label{eq:Mt}
+ M(t) \equiv \left[ N(t) - N_{\rm bkg} \right]\,\exp(+t / \tau_\mu) = N_0 \left[ 1 + A(t) \right].
+\end{equation}
+
+\begin{enumerate}
+ \setcounter{enumi}{2}
+ \item In order to extract $A(t)$ from $M(t)$, $N_0$ needs to be determined, which is almost the
+       most tricky part here. The idea is simple: since $A(t)$ is dominated by high frequency signals,
+       proper averaging over $M(t)$ should allow to determine $N_0$, assuming that $\langle A(t) \rangle = 0$.
+       Is this assumption always true? \emph{No!} For instance it is \emph{not} true if the averaging is preformed
+       over incomplete periodes of a single assumed signal. Another case where it will fail is if multiple signals
+       with too far apart frequencies is present, as \eg in the case of muonium. Said all this, let's come
+       back and try to determine $N_0$:
+\end{enumerate}
+
+\begin{equation}\label{eq:N0estimate}
+ N_0 = \sum_{k=0}^{N_{\rm avg}} w_k M(t_k),
+\end{equation}
+
+\noindent where $N_{\rm avg}$ is determined such that $N_{\rm avg} \Delta t \simeq 1 \mu$s ($\Delta t$ being the 
+time resolution. $1 \mu$s means averaging over many cyles). In order to get a good estimate for $N_{\rm avg}$, $N(t)$ is Fourier 
+transformed, and from this power spectrum the frequency with the largest amplitude is determined, $\nu_{\rm 0}$. From $\nu_0$, 
+$\Delta t$, the number of cycles fitting into $1 \mu$s can be determined, and from this and the time resolution $N_{\rm avg}$
+can be calculated. The weight $w_k$ is given by:
+
+\begin{equation}
+ w_k = \frac{\left[\Delta M(t_k)\right]^{-2}}{\sum_{j=0}^{N_{\rm avg}} \left[\Delta M(t_j)\right]^{-2}},
+\end{equation}
+
+\noindent where 
+
+\begin{equation}
+  \Delta M(t) = \left[ \left(\frac{\partial M}{\partial N} \Delta N\right)^2 + 
+                       \left(\frac{\partial M}{\partial N_{\rm bkg}} \Delta N_{\rm bkg}\right)^2 \right]^{1/2} 
+              \simeq \exp(+t/\tau_\mu) \sqrt{N(t)}.
+\end{equation} 
+
+\noindent The error estimate on $N_0$ is then
+
+\begin{equation}\label{eq:N0-rrf}
+ \Delta N_0 = \sigma_{N_0} = \sqrt{\sum_k w_k^2 \Delta M(t_k)^2}.
+\end{equation}
+
+\noindent Having estimated $N_0$, the asymmetry can be extracted as:
+
+\begin{equation}
+ A(t) = M(t) / N_0 - 1.
+\end{equation}
+
+\begin{enumerate}
+ \setcounter{enumi}{3}
+ \item Now the actual RRF transformation can take place: $A_{\rm rrf}(t) = 2 \times A(t) \cos(\omega_{\rm rrf} t + \phi_{\rm rrf})$. 
+       The factor of 2 is introduced to conserve the asymmetry amplitude. The idea is the following: Fourier transform theory tells as that
+\end{enumerate}
+
+\begin{equation}
+ {\cal F}\left\{2 \times A(t) \cos(\omega_{\rm rrf} t + \phi_{\rm rrf}) \right\} = 
+      {\cal F}\left\{A(t)\right\}(\omega-\omega_{\rm rrf}) + {\cal F}\left\{A(t)\right\}(\omega+\omega_{\rm rrf}),
+\end{equation}
+
+\noindent \ie that the Fourier spectrum of $A(t)$ is shifted down and up by $\omega - \omega_{\rm rrf}$ and $\omega + \omega_{\rm rrf}$, respectively.
+In order to get rid of the high frequency part (${\cal F}\left\{A(t)\right\}(\omega+\omega_{\rm rrf})$), $A_{\rm rrf}(t)$ will be heavily over-binned,
+\ie
+ 
+\begin{enumerate}
+ \setcounter{enumi}{4}
+ \item Do the rrf packing: $A_{\rm rrf}(t) \rightarrow \langle A_{\rm rrf}(t) \rangle_p$. Packing itself is a filtering of data! Especially this
+       kind of filter is dispersive \cite{King89}, \ie that it potentially is leading to line shape distortions. For symmetric, rather narrow
+       lines, this is unlikely to be a problem. However, this might be quite different for complex line shapes as in the case of vortex lattices.
+\end{enumerate}
+
+\noindent The property $\langle A_{\rm rrf}(t) \rangle_p$ is what is fitted. The error on this property is estimated the following way: (i) the 
+unpacked error of $A(t)$ is:
+
+\begin{equation}
+ \Delta A(t) \simeq \frac{\exp(+t/\tau_\mu)}{N_0}\,\left[ N(t) + \left( \frac{N(t)-N_{\rm bkg}}{N_0} \right)^2 \Delta N_0^2 \right]^{1/2},
+\end{equation}
+
+\noindent and form this the packed $A_{\rm rrf}(t)$ error can be calculated.
+
+\subsection{Asymmetry RRF Implementation}
+
+\begin{enumerate}
+ \item In order to circumvent the difficulties to estimate $N_0$ the asymmetry of the starting positron histograms is formed. For details 
+       see \cite{musrfit_userManual15}. For this, positron detectors geometrically under $180^\circ$ are used. However, due the the spiraling
+       of the positron in sufficiently high magnetic fields, and the uncertainties of the $t_0$'s, the geometrical phase might \emph{not}
+       correspond to the positron signal phase! At $B=9$T the uncertainty in $t_0$ by one channel leads to a phase shift of 
+       $\gamma_\mu B \Delta t \cdot (180 / \pi) = 1.7^\circ$. Fig.\ref{fig:hal-9500-t0} shows the $t_0$-region of a typical HAL-9500 spectrum.
+       It shows that it is very hard to get the absolut value of $t_0$ right.
+ \item Carry out the RRF transformation $A_{\rm rrf}(t) = 2 \times A(t) \cos(\omega_{\rm rrf} t + \phi_{\rm rrf})$.
+ \item Do the rrf packing.
+\end{enumerate}
+
+\begin{figure}[h]
+ \centering
+ \includegraphics[width=0.5\textwidth]{HAL-9500-t0.pdf}
+ \caption{The $t_0$ region of a typical HAL-9500 spectrum. The broad black hump with the green line, is the ``prompt'' peak.
+          It is \emph{not} straight forward how to define $t_0$.}\label{fig:hal-9500-t0}
+\end{figure}
+
+
+\section{Discussion}
+
+Both RRF transformation sketched above have weak points which makes it hard to estimate systematic errors. Both methods will fail at too
+low fields of $\lesssim 1$T. The only and single purpose of the RRF transformation is slughish computer power! We developed GPU based fitting
+which overcomes \emph{all} this uncontrolled weaknesses and henceforth RRF could be omitted altogether. I still added it for the time being,
+since strong GPU/CPU hardware is still a bit costly and therefore not affordable to everyone.
+
+In order to give a feeling about what might go ``wrong'' with the RRF, I was running a couple of test cases. The chosen asymmetry is
+
+\begin{equation}\label{eq:asymmetry-simulation}
+ A^{(j)}(t) =  A_0^{(j)} \sum_{k=1}^3 f_k \exp\left[-0.5\cdot (\sigma_k t)^2 \right] \cos(\gamma_\mu B_k t + \phi^{(j)}),
+\end{equation}
+
+\noindent with values found in Tab.\ref{tab:asymmetry-parameters}. For the simulation 4 positron detector signals were generated with 
+$A_0^{(j)} = \left\{ 0.2554, 0.2574, 0.2576, 0.2566 \right\}$. The further ingredients were: $N_0^{(j)} = \left\{ 27.0, 25.3, 25.6, 26.9 \right\}$,
+$N_{\rm bkg}^{(j)} = \left\{ 0.055, 0.060, 0.069, 0.064 \right\}$, and $ \phi^{(j)} = \left\{ 5.0, 95.0, 185.0, 275.0 \right\}$.
+
+\begin{table}[h]
+ \centering
+ \begin{tabular}{c|c|c|c}
+   $k$ & $f_k$ & $\sigma_k$ & $B_k$ \\ 
+       &       & ($1/\mu$s) & (T)   \\ \hline\hline
+    1  & 0.5   & 7          & $1$ or $9$ \\
+    2  & 0.2   & 0.75       & $1.02$ or $9.02$ \\
+    3  & 0.3   & 0.25       & $1.06$ or $9.06$
+ \end{tabular}
+ \caption{Parameters used in Eq.(\ref{eq:asymmetry-simulation}).}\label{tab:asymmetry-parameters}
+\end{table}
+ 
+\begin{figure}[h]
+ \centering
+ \includegraphics[width=0.45\textwidth]{08011-Fourier-Averaged.pdf} \quad
+ \includegraphics[width=0.45\textwidth]{08011-RRF-Histo-Fourier-Averaged-Ghost.pdf} \\
+ \includegraphics[width=0.45\textwidth]{08011-RRF-Asym-Fourier-Averaged-Ghost.pdf}
+ \caption{Averaged Fourier power spectra. Top left: from single histogram fit for the 1T data set. 
+          Top right: from single histogram RRF fit. Bottom: from asymmetry RRF fit. Both RRF
+          sets show ghost lines.}\label{fig:08011-Fourier}
+\end{figure}
+
+Figure.\ref{fig:08011-Fourier} shows the averaged Fourier power spectra for the simulated data sets at 1T. Both RRF transformation are
+showing ghost lines, even for optimally chosen RRF rebinning. At higher fields this is less pronounced. The ghost lines have various origins 
+such as aliasing effects due to the RRF packing not prefectly suppressing the high frequency part of $A_{\rm rrf}(t)$, leakage of the RRF frequency 
+for not sufficently precise known $N_0$ (see Eq.(\ref{eq:N0-rrf})) for single histogram RRF fits, etc.
+
+Fits of simulated data as described above (see Eq.(\ref{eq:asymmetry-simulation}), with fields 0.5, 1.0, 3.0, 5.0, 7.0, and 9.0T) show that above 
+about 1T the model parameters of the RRF fits are acceptable, but the error bars are typically about a factor 3 larger compared to single histogram
+fits. The asymmetries of the RRF fits are ``substantially'' too small. The $\chi^2$ values are close to meaningless for the RRF fits, since they
+are strongly depending on the RRF packing, time interval chosen, etc. 
+
+To summaries: RRF fits can be used for online analysis if no GPU accelerator is available, but \emph{must not} be used for any final analysis!
+
+\bibliographystyle{amsplain}
+\bibliography{rrf}
+
+\end{document}

doc/memos/rrf/rrf.bib

@@ -0,0 +1,29 @@
+@Article{ Riseman90,
+	title = {{The Rotating Reference Frame Transformation in $\mu$SR}},
+	author = "T. M. Riseman and J. H. Brewer",
+	journal = "Hyperfine Interact.",
+	volume = "65",
+	year = "1990",
+	pages = "1107"
+}
+
+@Misc{ HAL9500,
+	title = {{HAL-9500}},
+	author = "",
+	note = {{\verb!https://www.psi.ch/smus/hal-9500!}},
+}
+
+@book{ King89,
+  Address =      {New York},
+  Author =       {R. King and M. Ahmadi and R. Gorgui-Naguib and A. Kwabwe and M. Azimi-Sajadi},
+  Edition =      {1st},
+  Publisher =    {Plenum Press},
+  Title =        {Digital Filtering in one and two Dimensions},
+  Year =         1989
+}
+
+@Misc{ musrfit_userManual15,
+	title = {{Musrfit User Guide}},
+	author = "",
+	note = {{\verb!https://intranet.psi.ch/MUSR/MusrFit#A_5.3_Asymmetry_Fit!}},
+}

doc/musrfit.dox

@@ -6,8 +6,6 @@
 
   content:    Description of musrfit framework.
 
-  $Id$
-
 **********************************************************************************************/
 
 /**
@@ -18,18 +16,18 @@
 
 <p>People merely intrested in the handling of the programs should check this link:
 \htmlonly
-<a href="http://lmu.web.psi.ch/facilities/software/musrfit/user/MUSR/MusrFit.html">musrfit user manual</a>
+<a href="http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFit.html">musrfit user manual</a>
 \endhtmlonly
 \latexonly
-musrfit user manual: \texttt{http://lmu.web.psi.ch/facilities/software/musrfit/user/MUSR/MusrFit.html}
+musrfit user manual: \texttt{http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFit.html}
 \endlatexonly 
 
 <p>People which would like to know how to install the musrfit framework, please check this link:
 \htmlonly
-<a href="http://lmu.web.psi.ch/facilities/software/musrfit/user/MUSR/MusrFitSetup.html">How to setup musrfit on different platforms</a>
+<a href="http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFitSetup.html">How to setup musrfit on different platforms</a>
 \endhtmlonly
 \latexonly
-How to setup musrfit on different platforms: \texttt{http://lmu.web.psi.ch/facilities/software/musrfit/user/MUSR/MusrFitSetup.html}
+How to setup musrfit on different platforms: \texttt{http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFitSetup.html}
 \endlatexonly
 
 //****************************************************************************************************
@@ -40,6 +38,7 @@ How to setup musrfit on different platforms: \texttt{http://lmu.web.psi.ch/facil
 <p>The musrfit framework provies the following programs: 
 - \ref musrfit Carries out fits based on a msr-file.
 - \ref musrview Is used show the data in a graphical representation.
+- \ref musrFT Is used to show Fourier transforms of data without the need of a theory (raw data Fourier transform).
 - \ref musrt0 Is used to set graphically t0's, background and data ranges off raw histogram data.
 - \ref musrparam Can be used to generate ascii output files with extracted fit-parameters (from msr-files) and independent additional variables like temperature, field, ... The ascii output files can than be used to plot parameters, e.g. by gnuplot.
 - \ref msr2data A program (originally written by Bastian M. Wojek). Its purpose is to process/generate multiple musrfit msr-files with the same parameters and summarize the fitting results either in a TRIUMF DB or a column ASCII file.
@@ -77,26 +76,31 @@ This two points are somewhat contradictory, and currently it is not clear which
 
 \section bugs How to report bugs
 
-<p>Bugs, unexpected features, can be reported directly to me: \verbatim andreas.suter@psi.ch, \endverbatim or entered in the bug-tracking tool at PSI \verbatim https://tracker.intranet.psi.ch/ \endverbatim (access to within
-PSI firewall required).
+<p>Bugs, unexpected features, can be reported directly to me: \verbatim andreas.suter@psi.ch, \endverbatim or entered in the bug-tracking tool at bitbkucket \verbatim https://bitbucket.org/muonspin/musrfit/issues \endverbatim.
 
 //****************************************************************************************************
 \page musrfitPage
 \section musrfit musrfit
 
-<p>Here will eventually follow a more technical description of musrfit. If you looking for a user-manual like description, please check \htmlonly<a href="http://lmu.web.psi.ch/facilities/software/musrfit/user/MUSR/MusrFit.html">musrfit user manual</a>\endhtmlonly \latexonly musrfit user manual: \texttt{http://lmu.web.psi.ch/facilities/software/musrfit/user/MUSR/MusrFit.html} \endlatexonly
+<p>Here will eventually follow a more technical description of musrfit. If you looking for a user-manual like description, please check \htmlonly<a href="http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFit.html">musrfit user manual</a>\endhtmlonly \latexonly musrfit user manual: \texttt{http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFit.html} \endlatexonly
 
 //****************************************************************************************************
 \page musrviewPage
 \section musrview musrview
 
-<p>Here will eventually follow a more technical description of musrview. If you looking for a user-manual like description, please check \htmlonly<a href="http://lmu.web.psi.ch/facilities/software/musrfit/user/MUSR/MusrFit.html">musrfit user manual</a>\endhtmlonly \latexonly musrfit user manual: \texttt{http://lmu.web.psi.ch/facilities/software/musrfit/user/MUSR/MusrFit.html} \endlatexonly
+<p>Here will eventually follow a more technical description of musrview. If you looking for a user-manual like description, please check \htmlonly<a href="http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFit.html">musrfit user manual</a>\endhtmlonly \latexonly musrfit user manual: \texttt{http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFit.html} \endlatexonly
+
+//****************************************************************************************************
+\page musrFTPage
+\section musrFT musrFT
+
+<p>Here will eventually follow a more technical description of musrFT. If you looking for a user-manual like description, please check \htmlonly<a href="http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFit.html">musrfit user manual</a>\endhtmlonly \latexonly musrfit user manual: \texttt{http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFit.html} \endlatexonly
 
 //****************************************************************************************************
 \page musrt0Page
 \section musrt0 musrt0
 
-<p>Here will eventually follow a more technical description of musrt0. If you looking for a user-manual like description, please check \htmlonly<a href="http://lmu.web.psi.ch/facilities/software/musrfit/user/MUSR/MusrFit.html">musrfit user manual</a>\endhtmlonly \latexonly musrfit user manual: \texttt{http://lmu.web.psi.ch/facilities/software/musrfit/user/MUSR/MusrFit.html} \endlatexonly
+<p>Here will eventually follow a more technical description of musrt0. If you looking for a user-manual like description, please check \htmlonly<a href="http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFit.html">musrfit user manual</a>\endhtmlonly \latexonly musrfit user manual: \texttt{http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFit.html} \endlatexonly
 
 //****************************************************************************************************
 \page musrparamPage

doc/musrfit_dox.cfg

@@ -23,7 +23,7 @@ PROJECT_NAME           = musrfit
 # This could be handy for archiving the generated documentation or 
 # if some version control system is used.
 
-PROJECT_NUMBER         = 0.11.0
+PROJECT_NUMBER         = 0.14.0
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
 # base path where the generated documentation will be put. 
@@ -462,17 +462,19 @@ WARN_LOGFILE           =
 INPUT                  = musrfit.dox \
                          ../src/include/PFitterFcn.h \
                          ../src/include/PFitter.h \
-			 ../src/include/PFourier.h \
+                         ../src/include/PFourier.h \
+                         ../src/include/PFourierCanvas.h \
                          ../src/include/PFunctionGrammar.h \
                          ../src/include/PFunction.h \
                          ../src/include/PFunctionHandler.h \
-			 ../src/include/PMsr2Data.h \
+                         ../src/include/PMsr2Data.h \
                          ../src/include/PMsrHandler.h \
                          ../src/include/PMusrCanvas.h \
                          ../src/include/PMusrCanvasLinkDef.h \ 
                          ../src/include/PMusr.h \
-			 ../src/include/PMusrT0.h \
-			 ../src/include/PMusrT0LinkDef.h \
+                         ../src/include/PMusrT0.h \
+                         ../src/include/PMusrT0LinkDef.h \
+                         ../src/include/PPrepFourier.h \
                          ../src/include/PRunAsymmetry.h \
                          ../src/include/PRunBase.h \
                          ../src/include/PRunDataHandler.h \
@@ -488,7 +490,8 @@ INPUT                  = musrfit.dox \
                          ../src/include/PUserFcn.h \
                          ../src/classes/PFitter.cpp \
                          ../src/classes/PFitterFcn.cpp \
-			 ../src/classes/PFourier.cpp \
+                         ../src/classes/PFourier.cpp \
+                         ../src/classes/PFourierCanvas.cpp \
                          ../src/classes/PFunction.cpp \
                          ../src/classes/PFunctionHandler.cpp \
 			 ../src/classes/PMsr2Data.cpp \
@@ -496,6 +499,7 @@ INPUT                  = musrfit.dox \
                          ../src/classes/PMusrCanvas.cpp \
 			 ../src/classes/PMusr.cpp \
 			 ../src/classes/PMusrT0.cpp \
+                         ../src/classes/PPrepFourier.cpp \
                          ../src/classes/PRunAsymmetry.cpp \
                          ../src/classes/PRunBase.cpp \
                          ../src/classes/PRunDataHandler.cpp \

src/Makefile.am

@@ -16,31 +16,43 @@ if BUILD_MUSREDIT
   EDITORDIR = musredit
 endif
 
+if BUILD_MUSREDIT_QT5
+  EDITORDIR = musredit_qt5
+endif
+
 SUBDIRS = external/MusrRoot \
           external/TLemRunHeader \
           external/MuSR_software \
           external/mud \
           $(PNEXUSDIRS) \
           classes \
-          external
+          external \
+          musredit_qt5 \
+          musredit \
+          musrgui 
 
 if BUILD_MUSRGUI
-SUBDIRS += $(EDITORDIR)
+#SUBDIRS += $(EDITORDIR)
 EXTRA_DIST = $(EDITORDIR)/Makefile
 endif
 
 if BUILD_MUSREDIT
-SUBDIRS += $(EDITORDIR)
+#SUBDIRS += $(EDITORDIR)
 EXTRA_DIST = $(EDITORDIR)/Makefile
 endif
 
-bin_PROGRAMS = musrfit musrview musrt0 msr2msr msr2data any2many
+if BUILD_MUSREDIT_QT5
+EXTRA_DIST = $(EDITORDIR)/Makefile
+endif
+
+bin_PROGRAMS = musrfit musrview musrt0 musrFT msr2msr msr2data any2many
 bin_PROGRAMS += write_musrRoot_runHeader musrRootValidation
 bin_PROGRAMS += dump_header
 
 musrfit_SOURCES = musrfit.cpp
 musrview_SOURCES = musrview.cpp
 musrt0_SOURCES = musrt0.cpp
+musrFT_SOURCES = musrFT.cpp
 msr2msr_SOURCES = msr2msr.cpp
 msr2data_SOURCES = msr2data.cpp
 any2many_SOURCES = any2many.cpp
@@ -48,7 +60,7 @@ write_musrRoot_runHeader_SOURCES = write_musrRoot_runHeader.cpp
 musrRootValidation_SOURCES = musrRootValidation.cpp
 dump_header_SOURCES = dump_header.cpp
 
-xmldir = $(bindir)
+xmldir = $(HOME)/.musrfit
 xml_DATA = musrfit_startup.xml
 
 LIBADD = $(PMUSR_LIBS) $(MUSR_ROOT_LIBS) $(LEM_LIBS) $(PSIBIN_LIBS) $(MUD_LIBS) $(PNEXUS_LIBS)
@@ -70,7 +82,7 @@ install-xmlDATA: $(xml_DATA)
 	  DIFF="$$(diff "$(DESTDIR)$(xmldir)/$(xml_DATA)" "$(xml_DATA)" 2>&1)"; \
 	  if test "x$$DIFF" != "x"; then \
 	    echo "   " && \
-	    echo "   musrfit_startup.xml in $(bindir)" && \
+	    echo "   musrfit_startup.xml in $(xmldir)" && \
 	    echo "   is different from the distribution's version." && \
 	    echo "   Do you want to overwrite it? [y/N]" && \
 	    read OVERWRITE && \
@@ -89,7 +101,7 @@ uninstall-xmlDATA:
 	  DIFF="$$(diff "$(DESTDIR)$(xmldir)/$(xml_DATA)" "$(xml_DATA)" 2>&1)"; \
 	  if test "x$$DIFF" != "x"; then \
 	    echo "   " && \
-	    echo "   musrfit_startup.xml in $(bindir)" && \
+	    echo "   musrfit_startup.xml in $(xmldir)" && \
 	    echo "   is different from the distribution's version." && \
 	    echo "   Do you want to remove it? [y/N]" && \
 	    read REMOVE && \

src/any2many.cpp

@@ -54,7 +54,7 @@ using namespace std;
 void any2many_syntax()
 {
   cout << endl << "usage: any2many [--help]   : will show this help.";
-  cout << endl << "       any2many --version  : will show the svn version.";
+  cout << endl << "       any2many --version  : will show the git version.";
   cout << endl << "       any2many -f <filenameList-input> | -r <runList-input>";
   cout << endl << "                -c <convert-options> [-p <output-path>] [-y <year>]";
   cout << endl << "                [-o <outputFileName> | -t <in-template> <out-template>] [-s]";
@@ -83,6 +83,10 @@ void any2many_syntax()
   cout << endl << "                NeXus2-HDF4, NeXus2-HDF5, NeXus2-XML, WKM, ASCII";
   cout << endl << "                Comment: ROOT is superseeded by MusrRoot. If there is not a very good";
   cout << endl << "                reason, avoid it!";
+  cout << endl << "          -h <histo-group-list> : This option is for MusrRoot input files only!";
+  cout << endl << "                Select the the histo groups to be exported. <histo-group-list> is a space";
+  cout << endl << "                separated list of the histo group, e.g. -h 0, 20 will try to export the histo";
+  cout << endl << "                0 (NPP) and 20 (PPC).";
   cout << endl << "          -p <output-path> : where <output-path> is the output path for the";
   cout << endl << "               converted files. If nothing is given, the current directory";
   cout << endl << "               will be used, unless the option '-s' is used.";
@@ -190,7 +194,7 @@ int main(int argc, char *argv[])
 
   // call any2many --help or any2many --version
   if (argc == 2) {
-    if (strstr(argv[1], "--h"))
+    if (!strncmp(argv[1], "--help", 128))
       any2many_syntax();
     else if (strstr(argv[1], "--v")) {
 #ifdef HAVE_CONFIG_H
@@ -344,6 +348,21 @@ int main(int argc, char *argv[])
         show_syntax = true;
         break;
       }
+    } else if (!strcmp(argv[i], "-h")) { // filter histo group list (for MusrRoot and ROOT (LEM) only!)
+      bool done = false;
+      int j = i+1;
+      do {
+        status = sscanf(argv[j], "%d", &ival);
+        if (status == 1) {
+          info.groupHistoList.push_back(ival);
+          j++;
+        } else {
+          done = true;
+        }
+      } while (!done && (j<argc));
+      i = j-1;
+      if (j >= argc) // make sure that counter is still in range
+        break;
     } else if (!strcmp(argv[i], "-p")) { // filter output path name flag
       if (i+1 < argc) {
         info.outPath = argv[i+1];

src/classes/Makefile.am

@@ -4,6 +4,7 @@ h_sources = \
   ../include/PFitterFcn.h \
   ../include/PFitter.h \
   ../include/PFourier.h \
+  ../include/PFourierCanvas.h \
   ../include/PFunctionGrammar.h \
   ../include/PFunction.h \
   ../include/PFunctionHandler.h \
@@ -12,13 +13,16 @@ h_sources = \
   ../include/PMusrCanvas.h \
   ../include/PMusr.h \
   ../include/PMusrT0.h \
+  ../include/PPrepFourier.h \
   ../include/PRunAsymmetry.h \
+  ../include/PRunAsymmetryRRF.h \
   ../include/PRunBase.h \
   ../include/PRunDataHandler.h \
   ../include/PRunListCollection.h \
   ../include/PRunNonMusr.h \
   ../include/PRunMuMinus.h \
   ../include/PRunSingleHisto.h \
+  ../include/PRunSingleHistoRRF.h \
   ../include/PStartupHandler.h \
   ../include/PTheory.h
 
@@ -26,6 +30,7 @@ h_sources_userFcn = \
   ../include/PUserFcnBase.h
 
 h_linkdef = \
+  ../include/PFourierCanvasLinkDef.h \
   ../include/PMusrCanvasLinkDef.h \
   ../include/PMusrT0LinkDef.h \
   ../include/PStartupHandlerLinkDef.h
@@ -34,6 +39,7 @@ h_linkdef_userFcn = \
   ../include/PUserFcnBaseLinkDef.h
 
 dict_h_sources = \
+  PFourierCanvasDict.h \
   PMusrCanvasDict.h \
   PMusrT0Dict.h \
   PStartupHandlerDict.h
@@ -45,6 +51,7 @@ cpp_sources = \
   PFitter.cpp \
   PFitterFcn.cpp \
   PFourier.cpp \
+  PFourierCanvas.cpp \
   PFunction.cpp \
   PFunctionHandler.cpp \
   PMsr2Data.cpp \
@@ -52,13 +59,16 @@ cpp_sources = \
   PMusrCanvas.cpp \
   PMusr.cpp \
   PMusrT0.cpp \
+  PPrepFourier.cpp \
   PRunAsymmetry.cpp \
+  PRunAsymmetryRRF.cpp \
   PRunBase.cpp \
   PRunDataHandler.cpp \
   PRunListCollection.cpp \
   PRunNonMusr.cpp \
   PRunMuMinus.cpp \
   PRunSingleHisto.cpp \
+  PRunSingleHistoRRF.cpp \
   PStartupHandler.cpp \
   PTheory.cpp
 
@@ -66,6 +76,7 @@ cpp_sources_userFcn = \
   PUserFcnBase.cpp
 
 dict_cpp_sources = \
+  PFourierCanvasDict.cpp \
   PMusrCanvasDict.cpp \
   PMusrT0Dict.cpp \
   PStartupHandlerDict.cpp
@@ -84,7 +95,7 @@ AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS) -L@ROOTLIBDIR@
 CLEANFILES = *Dict.cpp *Dict.h *~ core
 
 %Dict.cpp %Dict.h: ../include/%.h ../include/%LinkDef.h
-	@ROOTCINT@ -v -f $*Dict.cpp -c -p $(INCLUDES) $^
+	@ROOTCINT@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
 
 lib_LTLIBRARIES = libPUserFcnBase.la libPMusr.la
 

src/classes/PFitter.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2014 by Andreas Suter                              *
+ *   Copyright (C) 2007-2016 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -1564,64 +1564,66 @@ Bool_t PFitter::ExecuteSave(Bool_t firstSave)
   }
 
   // handle expected chisq if applicable
-  if (fUseChi2) {
-    fParams = *(fRunInfo->GetMsrParamList()); // get the update parameters back
+  fParams = *(fRunInfo->GetMsrParamList()); // get the update parameters back
 
-    // calculate expected chisq
-    std::vector<Double_t> param;
-    Double_t totalExpectedChisq = 0.0;
-    std::vector<Double_t> expectedChisqPerHisto;
-    std::vector<UInt_t> ndfPerHisto;
+  // calculate expected chisq
+  std::vector<Double_t> param;
+  Double_t totalExpectedChisq = 0.0;
+  std::vector<Double_t> expectedChisqPerHisto;
+  std::vector<UInt_t> ndfPerHisto;
 
-    for (UInt_t i=0; i<fParams.size(); i++)
-      param.push_back(fParams[i].fValue);
+  for (UInt_t i=0; i<fParams.size(); i++)
+    param.push_back(fParams[i].fValue);
 
-    fFitterFcn->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerHisto);
+  // CalcExpectedChiSquare handles both, chisq and mlh
+  fFitterFcn->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerHisto);
 
-    // calculate chisq per run
-    std::vector<Double_t> chisqPerHisto;
-    for (UInt_t i=0; i<fRunInfo->GetMsrRunList()->size(); i++) {
+  // calculate chisq per run
+  std::vector<Double_t> chisqPerHisto;
+  for (UInt_t i=0; i<fRunInfo->GetMsrRunList()->size(); i++) {
+    if (fUseChi2)
       chisqPerHisto.push_back(fRunListCollection->GetSingleRunChisq(param, i));
-    }
-
-    if (totalExpectedChisq != 0.0) { // i.e. applicable for single histogram fits only
-      // get the ndf's of the histos
-      UInt_t ndf_histo;
-      for (UInt_t i=0; i<expectedChisqPerHisto.size(); i++) {
-        ndf_histo = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
-        ndfPerHisto.push_back(ndf_histo);
-      }
-
-      // feed the msr-file handler
-      PMsrStatisticStructure *statistics = fRunInfo->GetMsrStatistic();
-      if (statistics) {
-        statistics->fMinPerHisto = chisqPerHisto;
-        statistics->fMinExpected = totalExpectedChisq;
-        statistics->fMinExpectedPerHisto = expectedChisqPerHisto;
-        statistics->fNdfPerHisto = ndfPerHisto;
-      }
-    } else if (chisqPerHisto.size() > 1) { // in case expected chisq is not applicable like for asymmetry fits
-      UInt_t ndf_histo = 0;
-      for (UInt_t i=0; i<chisqPerHisto.size(); i++) {
-        ndf_histo = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
-        ndfPerHisto.push_back(ndf_histo);
-      }
-
-      // feed the msr-file handler
-      PMsrStatisticStructure *statistics = fRunInfo->GetMsrStatistic();
-      if (statistics) {
-        statistics->fMinPerHisto = chisqPerHisto;
-        statistics->fNdfPerHisto = ndfPerHisto;
-      }
-    }
-
-    // clean up
-    param.clear();
-    expectedChisqPerHisto.clear();
-    ndfPerHisto.clear();
-    chisqPerHisto.clear();
+    else
+      chisqPerHisto.push_back(fRunListCollection->GetSingleRunMaximumLikelihood(param, i));
   }
 
+  if (totalExpectedChisq != 0.0) { // i.e. applicable for single histogram fits only
+    // get the ndf's of the histos
+    UInt_t ndf_histo;
+    for (UInt_t i=0; i<expectedChisqPerHisto.size(); i++) {
+      ndf_histo = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+      ndfPerHisto.push_back(ndf_histo);
+    }
+
+    // feed the msr-file handler
+    PMsrStatisticStructure *statistics = fRunInfo->GetMsrStatistic();
+    if (statistics) {
+      statistics->fMinPerHisto = chisqPerHisto;
+      statistics->fMinExpected = totalExpectedChisq;
+      statistics->fMinExpectedPerHisto = expectedChisqPerHisto;
+      statistics->fNdfPerHisto = ndfPerHisto;
+    }
+  } else if (chisqPerHisto.size() > 1) { // in case expected chisq is not applicable like for asymmetry fits
+    UInt_t ndf_histo = 0;
+    for (UInt_t i=0; i<chisqPerHisto.size(); i++) {
+      ndf_histo = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+      ndfPerHisto.push_back(ndf_histo);
+    }
+
+    // feed the msr-file handler
+    PMsrStatisticStructure *statistics = fRunInfo->GetMsrStatistic();
+    if (statistics) {
+      statistics->fMinPerHisto = chisqPerHisto;
+      statistics->fNdfPerHisto = ndfPerHisto;
+    }
+  }
+
+  // clean up
+  param.clear();
+  expectedChisqPerHisto.clear();
+  ndfPerHisto.clear();
+  chisqPerHisto.clear();
+
   cout << ">> PFitter::ExecuteSave(): will write minuit2 output file ..." << endl;
 
   ofstream fout;