added a NPP, PPC switch and performed some clean-up

src/classes/PFitter.cpp

@@ -154,9 +154,11 @@ bool PFitter::DoFit()
         break;
       case PMN_MINOS:
         status = ExecuteMinos();
-        // set positive errors true
+        // set positive errors true if minos has been successfull
-        for (unsigned int i=0; i<fParams.size(); i++) {
+        if (status) {
-          fRunInfo->SetMsrParamPosErrorPresent(i, true);
+          for (unsigned int i=0; i<fParams.size(); i++) {
+            fRunInfo->SetMsrParamPosErrorPresent(i, true);
+          }
         }
         break;
       case PMN_PLOT:
@@ -366,10 +368,12 @@ bool PFitter::ExecuteMigrad()
   ROOT::Minuit2::FunctionMinimum min = migrad(maxfcn, tolerance);
   if (!min.IsValid()) {
     cout << endl << "**WARNING**: PFitter::ExecuteMigrad(): Fit did not converge, sorry ...";
+/*
     // set flag positive error present to false
     for (unsigned int i=0; i<fParams.size(); i++) {
       fRunInfo->SetMsrParamPosErrorPresent(i, false);
     }
+*/
     return false;
   }
 
@@ -435,10 +439,12 @@ bool PFitter::ExecuteMinimize()
   ROOT::Minuit2::FunctionMinimum min = minimize(maxfcn, tolerance); 
   if (!min.IsValid()) {
     cout << endl << "**WARNING**: PFitter::ExecuteMinimize(): Fit did not converge, sorry ...";
+/*
     // set flag positive error present to false
     for (unsigned int i=0; i<fParams.size(); i++) {
       fRunInfo->SetMsrParamPosErrorPresent(i, false);
     }
+*/
     return false;
   }
 

src/classes/PFunction.cpp

@@ -59,7 +59,7 @@ using namespace std;
  */
 PFunction::PFunction(tree_parse_info<> info)
 {
-  cout << endl << "in PFunction ...";
+//  cout << endl << "in PFunction ...";
 
   fInfo  = info;
 
@@ -528,7 +528,7 @@ void PFunction::EvalTreeForStringExpression(iter_t const& i)
   } else if (i->value.id() == PFunctionGrammar::termID) {
     termOp++;
     if (*i->value.begin() == '*') {
-cout << endl << ">> i->children.size() = " << i->children.size() << endl;
+//cout << endl << ">> i->children.size() = " << i->children.size() << endl;
       assert(i->children.size() == 2);
       EvalTreeForStringExpression(i->children.begin());
       fFuncString += " * ";

src/classes/PFunctionHandler.cpp

@@ -47,7 +47,7 @@ PFunctionHandler::PFunctionHandler(PMsrLines lines)
   fValid = true;
   fLines = lines;
 
-  cout << endl << "in PFunctionHandler(PMsrLines lines)";
+//  cout << endl << "in PFunctionHandler(PMsrLines lines)";
 }
 
 //-------------------------------------------------------------
@@ -59,7 +59,7 @@ PFunctionHandler::PFunctionHandler(PMsrLines lines)
  */
 PFunctionHandler::~PFunctionHandler()
 {
-  cout << endl << "in ~PFunctionHandler()" << endl << endl;
+//  cout << endl << "in ~PFunctionHandler()" << endl << endl;
 
   fLines.clear();
   fFuncs.clear();
@@ -74,7 +74,7 @@ PFunctionHandler::~PFunctionHandler()
  */
 bool PFunctionHandler::DoParse()
 {
-  cout << endl << "in PFunctionHandler::DoParse() ...";
+//  cout << endl << "in PFunctionHandler::DoParse() ...";
 
   bool success = true;
   PFunctionGrammar function;
@@ -82,7 +82,7 @@ bool PFunctionHandler::DoParse()
 
   // feed the function block into the parser. Start with i=1, since i=0 is FUNCTIONS
   for (unsigned int i=1; i<fLines.size(); i++) {
-cout << endl << "fLines[" << i << "] = '" << fLines[i].fLine.Data() << "'";
+// cout << endl << "fLines[" << i << "] = '" << fLines[i].fLine.Data() << "'";
 
     // function line to upper case
     line = fLines[i].fLine;
@@ -92,7 +92,7 @@ cout << endl << "fLines[" << i << "] = '" << fLines[i].fLine.Data() << "'";
     tree_parse_info<> info = ast_parse(line.Data(), function, space_p);
 
     if (info.full) {
-      cout << endl << "parse successful ..." << endl;
+//      cout << endl << "parse successful ..." << endl;
       PFunction func(info);
       fFuncs.push_back(func);
     } else {
@@ -115,10 +115,10 @@ cout << endl << "fLines[" << i << "] = '" << fLines[i].fLine.Data() << "'";
     }
   }
 
-  if (success) {
+//   if (success) {
-    for (unsigned int i=0; i<fFuncs.size(); i++)
+//     for (unsigned int i=0; i<fFuncs.size(); i++)
-      cout << endl << "func number = " << fFuncs[i].GetFuncNo();
+//       cout << endl << "func number = " << fFuncs[i].GetFuncNo();
-  }
+//   }
 
   return success;
 }

src/classes/PMusrCanvas.cpp

@@ -612,6 +612,7 @@ void PMusrCanvas::UpdateInfoPad()
     // energy if present
     tstr += TString("E=");
     dval = fRunList->GetEnergy(runs[runNo].fRunName);
+cout << endl << ">> dval = " << dval << " (Engery)";
     if (dval == -9.9e99) {
       tstr += TString("??,");
     } else {

src/classes/PRunDataHandler.cpp

@@ -161,9 +161,9 @@ bool PRunDataHandler::ReadFile()
       return false;
     // everything looks fine, hence try to read the data file
     if (!run_it->fFileFormat.CompareTo("root-npp")) // not post pile up corrected histos
-      success = ReadRootFile();
+      success = ReadRootFile(true);
     else if (!run_it->fFileFormat.CompareTo("root-ppc")) // post pile up corrected histos
-      success = ReadRootFile();
+      success = ReadRootFile(false);
     else if (!run_it->fFileFormat.CompareTo("nexus"))
       success = ReadNexusFile();
     else if (!run_it->fFileFormat.CompareTo("psi-bin"))
@@ -342,12 +342,15 @@ cout << endl << ">> generated path: " << str.Data() << endl;
 /**
  * <p>
  *
+ * \param notPostPileup This flag is used as a switch between "Not Post Pileup Corrected" 
+ *                      and "Post Pileup Corrected" histogramms.
  */
-bool PRunDataHandler::ReadRootFile()
+bool PRunDataHandler::ReadRootFile(bool notPostPileup)
 {
   PDoubleVector histoData;
   PRawRunData   runData;
 
+//cout << endl << ">> in ReadRootFile() ...";
   TFile f(fRunPathName.Data());
   if (f.IsZombie()) {
     return false;
@@ -379,6 +382,7 @@ bool PRunDataHandler::ReadRootFile()
 
   // get implantation energy
   runData.fEnergy = runHeader->GetImpEnergy();
+//cout << endl << ">> runData.fEnergy = " << runData.fEnergy;
 
   // get setup
   runData.fSetup = runHeader->GetLemSetup().GetString();
@@ -408,38 +412,42 @@ bool PRunDataHandler::ReadRootFile()
   }
   // get all the data
   char histoName[32];
-  // read first the data which are NOT post pileup corrected
+  if (notPostPileup) { // read the data which are NOT post pileup corrected
-  for (int i=0; i<noOfHistos; i++) {
+    for (int i=0; i<noOfHistos; i++) {
-    sprintf(histoName, "hDecay%02d", i);
+      sprintf(histoName, "hDecay%02d", i);
-    TH1F *histo = dynamic_cast<TH1F*>(folder->FindObjectAny(histoName));
+//cout << endl << ">> histoName = " << histoName;
-    if (!histo) {
+      TH1F *histo = dynamic_cast<TH1F*>(folder->FindObjectAny(histoName));
-      cout << endl << "PRunDataHandler::ReadRootFile: Couldn't get histo " << histoName;
+      if (!histo) {
-      return false;
+        cout << endl << "PRunDataHandler::ReadRootFile: Couldn't get histo " << histoName;
+        return false;
+      }
+      // fill data
+      for (int j=1; j<histo->GetNbinsX(); j++)
+        histoData.push_back(histo->GetBinContent(j));
+      // store them in runData vector
+      runData.fDataBin.push_back(histoData);
+      // clear histoData for the next histo
+      histoData.clear();
     }
-    // fill data
+  } else { // read the data which ARE post pileup corrected
-    for (int j=1; j<histo->GetNbinsX(); j++)
+    for (int i=0; i<noOfHistos; i++) {
-      histoData.push_back(histo->GetBinContent(j));
+      sprintf(histoName, "hDecay%02d", i+POST_PILEUP_HISTO_OFFSET);
-    // store them in runData vector
+//cout << endl << ">> histoName = " << histoName;
-    runData.fDataBin.push_back(histoData);
+      TH1F *histo = dynamic_cast<TH1F*>(folder->FindObjectAny(histoName));
-    // clear histoData for the next histo
+      if (!histo) {
-    histoData.clear();
+        cout << endl << "PRunDataHandler::ReadRootFile: Couldn't get histo " << histoName;
-  }
+        return false;
-  // now read the data which ARE post pileup corrected
+      }
-  for (int i=0; i<noOfHistos; i++) {
+      // fill data
-    sprintf(histoName, "hDecay%02d", i+POST_PILEUP_HISTO_OFFSET);
+      for (int j=1; j<histo->GetNbinsX(); j++)
-    TH1F *histo = dynamic_cast<TH1F*>(folder->FindObjectAny(histoName));
+        histoData.push_back(histo->GetBinContent(j));
-    if (!histo) {
+      // store them in runData vector
-      cout << endl << "PRunDataHandler::ReadRootFile: Couldn't get histo " << histoName;
+      runData.fDataBin.push_back(histoData);
-      return false;
+      // clear histoData for the next histo
+      histoData.clear();
     }
-    // fill data
-    for (int j=1; j<histo->GetNbinsX(); j++)
-      histoData.push_back(histo->GetBinContent(j));
-    // store them in runData vector
-    runData.fDataBin.push_back(histoData);
-    // clear histoData for the next histo
-    histoData.clear();
   }
+//cout << endl;
 
   f.Close();
 

src/classes/PRunListCollection.cpp

@@ -92,11 +92,11 @@ bool PRunListCollection::Add(int runNo, EPMusrHandleTag tag)
 {
   bool success = true;
 
-  PMsrRunStructure *runList = &(*fMsrInfo->GetMsrRunList())[runNo];
+//  PMsrRunStructure *runList = &(*fMsrInfo->GetMsrRunList())[runNo];
 
-  cout << endl << "PRunListCollection::Add(): will add run no " << runNo;
+//   cout << endl << "PRunListCollection::Add(): will add run no " << runNo;
-  cout << ", name = " << runList->fRunName.Data();
+//   cout << ", name = " << runList->fRunName.Data();
-  cout << ", type = " << runList->fFitType;
+//   cout << ", type = " << runList->fFitType;
 
   int fitType = (*fMsrInfo->GetMsrRunList())[runNo].fFitType;
 

src/classes/PTheory.cpp

@@ -185,7 +185,7 @@ PTheory::PTheory(PMsrHandler *msrInfo, unsigned int runNo, const bool hasParent)
 
     // if userFcn, the first entry is the function name and needs to be handled specially
     if ((fType == THEORY_USER_FCN) && ((i == 1) || (i == 2))) {
-cout << endl << ">> userFcn: i=" << i << ", str=" << str.Data() << endl;
+//cout << endl << ">> userFcn: i=" << i << ", str=" << str.Data() << endl;
       if (i == 1) {
         fUserFcnSharedLibName = str;
       }
@@ -282,7 +282,7 @@ cout << endl << ">> userFcn: i=" << i << ", str=" << str.Data() << endl;
     // invoke user function object
     fUserFcn = 0;
     fUserFcn = (PUserFcnBase*)TClass::GetClass(fUserFcnClassName.Data())->New();
-cout << endl << ">> fUserFcn = " << fUserFcn << endl;
+//cout << endl << ">> fUserFcn = " << fUserFcn << endl;
     if (fUserFcn == 0) {
       cout << endl << "**ERROR**: PTheory: user function object could not be invoked. See line no " << line->fLineNo;
       fValid = false;
@@ -690,7 +690,7 @@ void PTheory::MakeCleanAndTidyTheoryBlock(PMsrLines *fullTheoryBlock)
       str.Resize(index);
     // tokenize line
     tokens = str.Tokenize(" \t");
-cout << endl << ">> #tokens=" << tokens->GetEntries() << ", str=" << str.Data();
+//cout << endl << ">> #tokens=" << tokens->GetEntries() << ", str=" << str.Data();
     // make a handable string out of the asymmetry token
     ostr = dynamic_cast<TObjString*>(tokens->At(0));
     str = ostr->GetString();
@@ -765,7 +765,7 @@ void PTheory::MakeCleanAndTidyPolynom(unsigned int i, PMsrLines *fullTheoryBlock
   TObjString *ostr;
   char substr[256];
 
-cout << endl << ">> MakeCleanAndTidyPolynom: " << (*fullTheoryBlock)[i].fLine.Data();
+//cout << endl << ">> MakeCleanAndTidyPolynom: " << (*fullTheoryBlock)[i].fLine.Data();
 
   // init tidy
   tidy = TString("polynom ");
@@ -811,7 +811,7 @@ void PTheory::MakeCleanAndTidyUserFcn(unsigned int i, PMsrLines *fullTheoryBlock
   TObjArray *tokens = 0;
   TObjString *ostr;
 
-cout << endl << ">> MakeCleanAndTidyUserFcn: " << (*fullTheoryBlock)[i].fLine.Data();
+//cout << endl << ">> MakeCleanAndTidyUserFcn: " << (*fullTheoryBlock)[i].fLine.Data();
 
   // init tidy
   tidy = TString("userFcn ");
@@ -1448,6 +1448,7 @@ double PTheory::Polynom(register double t, const PDoubleVector& paramValues, con
  */
 double PTheory::UserFcn(register double t, const PDoubleVector& paramValues, const PDoubleVector& funcValues) const
 {
+/*
 static bool first = true;
 if (first) {
   cout << endl << ">> UserFcn: fParamNo.size()=" << fParamNo.size() << ", fUserParam.size()=" << fUserParam.size();
@@ -1456,6 +1457,7 @@ if (first) {
   }
   cout << endl;
 }
+*/
 
   // check if FUNCTIONS are used
   for (unsigned int i=0; i<fUserParam.size(); i++) {
@@ -1466,6 +1468,7 @@ if (first) {
     }
   }
 
+/*
 if (first) {
   first = false;
   for (unsigned int i=0; i<fUserParam.size(); i++) {
@@ -1475,6 +1478,6 @@ if (first) {
   cout << endl << ">> t=" << t << ", function value=" << (*fUserFcn)(t, fUserParam);
   cout << endl;
 }
-
+*/
   return (*fUserFcn)(t, fUserParam);
 }

src/include/PRunDataHandler.h

@@ -62,7 +62,7 @@ class PRunDataHandler
     virtual bool ReadFile();
     virtual bool FileAlreadyRead(PMsrRunStructure &runInfo);
     virtual bool FileExistsCheck(PMsrRunStructure &runInfo);
-    virtual bool ReadRootFile();
+    virtual bool ReadRootFile(bool notPostPileup);
     virtual bool ReadNexusFile();
     virtual bool ReadNemuFile();
     virtual bool ReadPsiBinFile();

src/tests/fourier/PMusrFourier.cpp

@@ -505,6 +505,7 @@ void PMusrFourier::ApodizeData(int apodizationTag) {
 
   switch (apodizationTag) {
     case F_APODIZATION_NONE:
+      return;
       break;
     case F_APODIZATION_WEAK:
       c[0] = cweak[0]+cweak[1]+cweak[2];

src/tests/fourier/fourier.cpp

@@ -185,7 +185,7 @@ cout << endl << "#bins=" << histo->GetNbinsX();
 
     cout << endl << ">> Do you wish to apodize your data (y/n)? ";
     cin >> answer;
-    unsigned int apodizationTag=0;
+    unsigned int apodizationTag = F_APODIZATION_NONE;
     if (strstr(answer, "y")) {
       cout << endl << ">> apodization (1=weak, 2=medium, 3=strong, 4=user) = ";
       cin >> apodizationTag;

src/tests/rootMinuit2Test/minuit2test.C

@@ -78,17 +78,17 @@ void minuit2test()
   // set parameters
   gFitFcn->SetParNames("N0", "asym", "lambda", "B", "phase", "Bkg");
   gFitFcn->SetParameter(0, 30.0);   // N0
-//  gFitFcn->SetParLimits(0, 0.0, 1.0e6);
+  gFitFcn->SetParLimits(0, 0.0, 1.0e6);
   gFitFcn->SetParameter(1, 0.26);    // asym
-//  gFitFcn->SetParLimits(1, 0.0, 0.33);
+  gFitFcn->SetParLimits(1, 0.0, 0.33);
   gFitFcn->SetParameter(2, 0.3);     // lambda
-//  gFitFcn->SetParLimits(2, 0.0, 100.0);
+  gFitFcn->SetParLimits(2, 0.0, 100.0);
   gFitFcn->SetParameter(3, 100.0);   // B
-//  gFitFcn->SetParLimits(3, 0.0, 1000.0);
+  gFitFcn->SetParLimits(3, 0.0, 1000.0);
   gFitFcn->SetParameter(4, 0.0);     // phase
-//  gFitFcn->SetParLimits(4, -90.0, 90.0);
+  gFitFcn->SetParLimits(4, -90.0, 90.0);
   gFitFcn->SetParameter(5, 5.0);    // Bkg
-//  gFitFcn->SetParLimits(5, 0.0, 1000.0);
+  gFitFcn->SetParLimits(5, 0.0, 1000.0);
 
   cout << endl << "gFitFcn->Integral(0.0, 12.0) = " << gFitFcn->Integral(0.0, 12.0);
   cout << endl;
@@ -100,9 +100,13 @@ void minuit2test()
 
   histo->Draw();
 
-  gFitFcn->SetParameter(0, 150.0);   // N0
+  gFitFcn->SetParameter(0, 1000.0); // N0
-  gFitFcn->SetParameter(5, 23.0);    // Bkg
+  gFitFcn->SetParameter(1, 0.1);    // asym
+  gFitFcn->SetParameter(2, 1.0);    // lambda
+  gFitFcn->SetParameter(3, 50.0);   // B
+  gFitFcn->SetParameter(4, 0.0);    // phase
+  gFitFcn->SetParameter(5, 300.0);  // Bkg
   
   TVirtualFitter::SetDefaultFitter("Minuit2");
-  histo->Fit("gFitFcn", "L"); // L->likleyhood, E->minos 
+  histo->Fit("gFitFcn", ""); // L->likleyhood, E->minos 
 }