Added the musrfit --title-from-data-file option to msr2data (-t) and made TFitPofB compilable with g++-4.4

configure.ac

@@ -220,7 +220,7 @@ AC_SUBST(ROOT_CFLAGS)
 # It should be checked properly for -lMinuit2 -- at the moment we simply look if a header file is present in the include directory:
 
 AC_CHECK_FILE([${ROOTINCDIR}/../include/Minuit2/MnMinimize.h], AC_MSG_RESULT([Minuit2 headers found... OK]),
-  AC_MSG_ERROR([Minuit2 headers not found... Please check!]))
+  AC_MSG_WARN([Minuit2 headers not found... Please check!]))
 
 
 dnl -----------------------------------------------

src/external/TFitPofB-lib/classes/Makefile.TFitPofB

@@ -6,14 +6,14 @@ ROOTCFLAGS    = $(shell $(ROOTSYS)/bin/root-config --cflags)
 #---------------------------------------------------
 
 OS            = LINUX
-CXX           = g++-4.2.4
+CXX           = g++-4.4.0
 CXXFLAGS      = -O3 -Wall -fopenmp -Wno-trigraphs -fPIC
 MUSRFITINCLUDE = ../../../include
 #MUSRFITINCLUDE = /home/l_wojek/rep/analysis/musrfit/src/include
 LOCALINCLUDE  = ../include
 ROOTINCLUDE   = $(ROOTSYS)/include
 INCLUDES      = -I$(LOCALINCLUDE) -I$(MUSRFITINCLUDE) -I$(ROOTINCLUDE)
-LD            = g++-4.2.4
+LD            = g++-4.4.0
 LDFLAGS       = -O3
 SOFLAGS       = -O3 -shared -fopenmp -lfftw3_threads -lfftw3 -lm -lpthread
 

src/external/TFitPofB-lib/classes/TFitPofBStartupHandler.cpp

@@ -33,6 +33,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
+#include <cstdlib>
 #include <iostream>
 using namespace std;
 

src/external/TFitPofB-lib/classes/TLondon1D.cpp

@@ -140,7 +140,7 @@ TLondon1D3LSub::~TLondon1D3LSub() {
 // creates (a pointer to) the TPofTCalc object (with the FFT plan)
 //------------------
 
-TLondon1DHS::TLondon1DHS() : fCalcNeeded(true), fFirstCall(true), fDeadLayerChanged(true) {
+TLondon1DHS::TLondon1DHS() : fCalcNeeded(true), fFirstCall(true) {
 
     // read startup file
     string startup_path_name("TFitPofB_startup.xml");
@@ -618,7 +618,7 @@ TProximity1D1LHS::TProximity1D1LHS() : fCalcNeeded(true), fFirstCall(true) {
     fParForPofB.push_back(startupHandler->GetDeltaB());
     fParForPofB.push_back(0.0);
     fParForPofB.push_back(0.0); // Bkg-Field
-    fParForPofB.push_back(0.005); // Bkg-width
+    fParForPofB.push_back(0.01); // Bkg-width
     fParForPofB.push_back(0.0); // Bkg-weight
 
     TTrimSPData *x = new TTrimSPData(rge_path, energy_vec);
@@ -669,7 +669,7 @@ double TProximity1D1LHS::operator()(double t, const vector<double> &par) const {
       fParForBofZ.push_back(fPar[i]);
 //      cout << "fParForBofZ[" << i-2 << "] = " << fParForBofZ[i-2] << endl;
     }
-    fFirstCall=false;
+    fFirstCall = false;
     width_changed = true;
     dead_layer_changed = true;
 //  cout << this << endl;

src/external/TFitPofB-lib/classes/TPofBCalc.cpp

@@ -11,6 +11,7 @@
 
 #include "TPofTCalc.h"
 #include <cmath>
+#include <cstdlib>
 #include <iostream>
 #include <fstream>
 #include <cassert>

src/external/TFitPofB-lib/classes/TPofTCalc.cpp

@@ -40,6 +40,7 @@
 #include <cmath>
 #include <iostream>
 #include <cstdio>
+#include <cstdlib>
 
 #include <omp.h>
 

src/external/TFitPofB-lib/classes/TSkewedGss.cpp

@@ -0,0 +1,149 @@
+/***************************************************************************
+
+  TSkewedGss.cpp
+
+  Author: Bastian M. Wojek
+  e-mail: bastian.wojek@psi.ch
+
+  2009/01/24
+
+***************************************************************************/
+
+#include "TSkewedGss.h"
+#include <iostream>
+#include <cassert>
+using namespace std;
+
+#include <TSAXParser.h>
+#include "TFitPofBStartupHandler.h"
+
+ClassImp(TSkewedGss)
+
+//------------------
+// Destructor of the TSkewedGss class -- cleaning up
+//------------------
+
+TSkewedGss::~TSkewedGss() {
+    fPar.clear();
+    fParForPofB.clear();
+    fParForPofT.clear();
+    delete fPofT;
+    fPofT = 0;
+}
+
+//------------------
+// Constructor of the TSkewedGss class -- creates (a pointer to) the TPofTCalc object (with the FFT plan)
+//------------------
+
+TSkewedGss::TSkewedGss() : fCalcNeeded(true), fFirstCall(true) {
+
+    // read startup file
+    string startup_path_name("TFitPofB_startup.xml");
+
+    TSAXParser *saxParser = new TSAXParser();
+    TFitPofBStartupHandler *startupHandler = new TFitPofBStartupHandler();
+    saxParser->ConnectToHandler("TFitPofBStartupHandler", startupHandler);
+    int status (saxParser->ParseFile(startup_path_name.c_str()));
+    // check for parse errors
+    if (status) { // error
+      cout << endl << "**WARNING** reading/parsing TFitPofB_startup.xml failed." << endl;
+    }
+
+    fWisdom = startupHandler->GetWisdomFile();
+
+    fParForPofT.push_back(0.0); // phase
+    fParForPofT.push_back(startupHandler->GetDeltat());
+    fParForPofT.push_back(startupHandler->GetDeltaB());
+
+    fParForPofB.push_back(startupHandler->GetDeltat());
+    fParForPofB.push_back(startupHandler->GetDeltaB());
+    fParForPofB.push_back(0.0); // nu0
+    fParForPofB.push_back(0.0); // s-
+    fParForPofB.push_back(0.0); // s+
+
+    TPofTCalc *y = new TPofTCalc(fWisdom, fParForPofT);
+    fPofT = y;
+    y = 0;
+    delete y;
+
+    // clean up
+    if (saxParser) {
+      delete saxParser;
+      saxParser = 0;
+    }
+    if (startupHandler) {
+      delete startupHandler;
+      startupHandler = 0;
+    }
+}
+
+//------------------
+// TSkewedGss-Method that calls the procedures to create p(B) and P(t)
+// It finally returns P(t) for a given t.
+// Parameters: all the parameters for the function to be fitted through TSkewedGss (phase,freq0,sigma-,sigma+)
+//------------------
+
+double TSkewedGss::operator()(double t, const vector<double> &par) const {
+
+  assert(par.size() == 4);
+
+  if(t<0.0)
+    return 1.0;
+
+  // check if the function is called the first time and if yes, read in parameters
+
+  if(fFirstCall){
+    fPar = par;
+    fFirstCall=false;
+  }
+
+  // check if any parameter has changed
+
+  bool par_changed(false);
+  bool only_phase_changed(false);
+
+  for (unsigned int i(0); i<fPar.size(); i++) {
+    if( fPar[i]-par[i] ) {
+      fPar[i] = par[i];
+      par_changed = true;
+      if (i == 0) {
+        only_phase_changed = true;
+      } else {
+        only_phase_changed = false;
+      }
+    }
+  }
+
+  if (par_changed)
+    fCalcNeeded = true;
+
+  // if model parameters have changed, recalculate P(B) and P(t)
+
+  if (fCalcNeeded) {
+
+    fParForPofT[0] = par[0]; // phase
+
+    if(!only_phase_changed) {
+
+//      cout << " Parameters have changed, (re-)calculating p(B) and P(t) now..." << endl;
+
+      fParForPofB[2] = par[1]; // nu0
+      fParForPofB[3] = par[2]; // sigma-
+      fParForPofB[4] = par[3]; // sigma+
+
+      TPofBCalc PofB("skg", fParForPofB);
+      fPofT->DoFFT(PofB);
+
+    }/* else {
+      cout << "Only the phase parameter has changed, (re-)calculating P(t) now..." << endl;
+    }*/
+
+    fPofT->CalcPol(fParForPofT);
+
+    fCalcNeeded = false;
+  }
+
+  return fPofT->Eval(t);
+
+}
+

src/external/TFitPofB-lib/include/TSkewedGss.h

@@ -0,0 +1,39 @@
+/***************************************************************************
+
+  TSkewedGss.h
+
+  Author: Bastian M. Wojek
+  e-mail: bastian.wojek@psi.ch
+
+  2009/01/24
+
+***************************************************************************/
+
+#ifndef _TSkewedGss_H_
+#define _TSkewedGss_H_
+
+#include "PUserFcnBase.h"
+#include "TPofTCalc.h"
+
+class TSkewedGss : public PUserFcnBase {
+
+public:
+  // default constructor
+  TSkewedGss();
+  ~TSkewedGss();
+
+  double operator()(double, const vector<double>&) const;
+
+private:
+  mutable vector<double> fPar;
+  TPofTCalc *fPofT;
+  mutable bool fCalcNeeded;
+  mutable bool fFirstCall;
+  mutable vector<double> fParForPofT;
+  mutable vector<double> fParForPofB;
+  string fWisdom;
+
+  ClassDef(TSkewedGss,1)
+};
+
+#endif //_TSkewedGss_H_

src/external/scripts/msr2data

@@ -11,11 +11,11 @@ if [ "$#" -lt 2 ] ; then
 
         "musrfit-msr to db/dat converter"
 
-USAGE:   msr2data FIRSTRUN# LASTRUN# EXTENSION [noheader | nosummary | fit-TEMPLATERUN# | -oOUTPUT_FILE | -k | data ]
+USAGE:   msr2data FIRSTRUN# LASTRUN# EXTENSION [noheader | nosummary | fit-TEMPLATERUN# | -oOUTPUT_FILE | -k | -t | data ]
          OR
-         msr2data \[SPACE SEPARATED LIST OF RUNS\] EXTENSION [noheader | nosummary | fit-TEMPLATERUN# | -oOUTPUT_FILE | -k | data ]
+         msr2data \[SPACE SEPARATED LIST OF RUNS\] EXTENSION [noheader | nosummary | fit-TEMPLATERUN# | -oOUTPUT_FILE | -k | -t | data ]
          OR
-         msr2data RUNLISTFILE EXTENSION [noheader | nosummary | fit-TEMPLATERUN# | -oOUTPUT_FILE | -k | data ]
+         msr2data RUNLISTFILE EXTENSION [noheader | nosummary | fit-TEMPLATERUN# | -oOUTPUT_FILE | -k | -t | data ]
 
 This small script converts subsequent musrfit msr output files into one db- or column-ASCII-file using bash/awk.
 
@@ -61,6 +61,8 @@ template for the first musrfit input file. The results of the fits will be writt
 
 For keeping the MINUIT2 output files after calling musrfit, i.e. invoke musrfit with the option "--keep-mn2-output" just pass the option "-k" to msr2data. If you pass this option to msr2data but do not fit any data, the option will just be ignored.
 
+If musrfit should add the title present in the first data file mentioned in a RUN block to the title line of the mlog output file, pass the option "-t" to msr2data. Then musrfit is called with the option "--title-from-data-file". If you pass this option to msr2data but do not fit any data, the option will just be ignored.
+
 If your musrfit output files do not have an extension as specified above like "200.msr" you have to call the script as in the following example.
 
 Example 5:
@@ -283,7 +285,15 @@ else
       for PAR in "$@"
       do
         if [ "$PAR" == "-k" ]; then
-          MUSRFITPARAM="-k"
+          MUSRFITPARAM+=" -k"
+          break
+        fi
+      done
+
+      for PAR in "$@"
+      do
+        if [ "$PAR" == "-t" ]; then
+          MUSRFITPARAM+=" -t"
           break
         fi
       done
@@ -395,7 +405,7 @@ else
       if [ "${CUR_PAR:0:2}" == "-o" ]; then
         if [ "$CUR_PAR" == "-o" ]; then
           if [ "$l" -ne "$LAST_OPT_PAR" ] && [ "$NEXT_PAR" != "noheader" ] && [ "$NEXT_PAR" != "nosummary" ] \
-          && [ "${NEXT_PAR:0:3}" != "fit" ] && [ "$NEXT_PAR" != "-k" ]; then
+          && [ "${NEXT_PAR:0:3}" != "fit" ] && [ "$NEXT_PAR" != "-k" ] && [ "$NEXT_PAR" != "-t" ]; then
             OUTFILE=$NEXT_PAR
             break
           else