updated the ChangeLog.

CMakeLists.txt

@@ -5,7 +5,7 @@ if (CMAKE_VERSION GREATER_EQUAL 3.12)
   cmake_policy(SET CMP0075 NEW)
 endif (CMAKE_VERSION GREATER_EQUAL 3.12)
 
-project(musrfit VERSION 1.7.2 LANGUAGES C CXX)
+project(musrfit VERSION 1.7.4 LANGUAGES C CXX)
 
 #--- musrfit specific options -------------------------------------------------
 option(nexus "build optional NeXus support. Needed for ISIS" OFF)

ChangeLog

@@ -12,6 +12,17 @@ or
 
 https://bitbucket.org/muonspin/musrfit/commits/all
 
+Release of V1.7.4, 2021/06/16
+=============================
+
+allow in asymmetry fits #forward groups != #backward groups
+
+Release of V1.7.3, 2021/06/01
+=============================
+
+making musrfit Apple Silicon M1 ready. Currently there is still an open issue 
+with NeXus (HDF4 only).
+
 Release of V1.7.2, 2021/04/16
 =============================
 

src/classes/PMsrHandler.cpp

@@ -6335,15 +6335,6 @@ Bool_t PMsrHandler::CheckHistoGrouping()
   Bool_t result = true;
 
   for (UInt_t i=0; i<fRuns.size(); i++) {    
-    if (fRuns[i].GetFitType() == MSR_FITTYPE_ASYM || fRuns[i].GetFitType() == MSR_FITTYPE_BNMR) {
-      if (fRuns[i].GetForwardHistoNoSize() != fRuns[i].GetBackwardHistoNoSize()) {
-        std::cerr << std::endl << ">> PMsrHandler::CheckHistoGrouping: **ERROR** # of forward histos != # of backward histos.";
-        std::cerr << std::endl << ">> Run #" << i+1;
-        std::cerr << std::endl;
-        result = false;
-        break;
-      }
-    }
     // check grouping entries are not identical, e.g. forward 1 1 2
     if (fRuns[i].GetForwardHistoNoSize() > 1) {
       for (UInt_t j=0; j<fRuns[i].GetForwardHistoNoSize(); j++) {

src/classes/PRunAsymmetry.cpp

@@ -602,16 +602,6 @@ Bool_t PRunAsymmetry::PrepareData()
       return false;
     }
   }
-  if (forwardHistoNo.size() != backwardHistoNo.size()) {
-    std::cerr << std::endl << ">> PRunAsymmetry::PrepareData(): **PANIC ERROR**:";
-    std::cerr << std::endl << ">> # of forward histograms different from # of backward histograms.";
-    std::cerr << std::endl << ">> Will quit :-(";
-    std::cerr << std::endl;
-    // clean up
-    forwardHistoNo.clear();
-    backwardHistoNo.clear();
-    return false;
-  }
   
   // keep the time resolution in (us)
   fTimeResolution = runData->GetTimeResolution()/1.0e3;
@@ -626,11 +616,13 @@ Bool_t PRunAsymmetry::PrepareData()
   // keep the histo of each group at this point (addruns handled below)
   std::vector<PDoubleVector> forward, backward;
   forward.resize(forwardHistoNo.size());   // resize to number of groups
-  backward.resize(backwardHistoNo.size()); // resize to numer of groups
   for (UInt_t i=0; i<forwardHistoNo.size(); i++) {
     forward[i].resize(runData->GetDataBin(forwardHistoNo[i])->size());
-    backward[i].resize(runData->GetDataBin(backwardHistoNo[i])->size());
     forward[i]  = *runData->GetDataBin(forwardHistoNo[i]);
+  }
+  backward.resize(backwardHistoNo.size()); // resize to number of groups
+  for (UInt_t i=0; i<backwardHistoNo.size(); i++) {
+    backward[i].resize(runData->GetDataBin(backwardHistoNo[i])->size());
     backward[i] = *runData->GetDataBin(backwardHistoNo[i]);
   }
 
@@ -676,9 +668,11 @@ Bool_t PRunAsymmetry::PrepareData()
 
   // set forward/backward histo data of the first group
   fForward.resize(forward[0].size());
-  fBackward.resize(backward[0].size());
   for (UInt_t i=0; i<fForward.size(); i++) {
     fForward[i]  = forward[0][i];
+  }
+  fBackward.resize(backward[0].size());
+  for (UInt_t i=0; i<fBackward.size(); i++) {
     fBackward[i] = backward[0][i];
   }
 
@@ -781,7 +775,21 @@ Bool_t PRunAsymmetry::PrepareData()
  */
 Bool_t PRunAsymmetry::SubtractFixBkg()
 {
+  if (fRunInfo->GetBkgFix(0) == PMUSR_UNDEFINED) {
+    std::cerr << "PRunAsymmetry::SubtractFixBkg(): **ERROR** no fixed bkg for forward set. Will do nothing here." << std::endl;
+    return false;
+  }
+  if (fRunInfo->GetBkgFix(1) == PMUSR_UNDEFINED) {
+    std::cerr << "PRunAsymmetry::SubtractFixBkg(): **ERROR** no fixed bkg for backward set. Will do nothing here." << std::endl;
+    std::cerr << "   you need an entry like:" << std::endl;
+    std::cerr << "   backgr.fix      2  3" << std::endl;
+    std::cerr << "   i.e. two entries for forward and backward." << std::endl;
+    return false;
+  }
+
+
   Double_t dval;
+
   for (UInt_t i=0; i<fForward.size(); i++) {
     // keep the error, and make sure that the bin is NOT empty
     if (fForward[i] != 0.0)
@@ -1005,8 +1013,8 @@ Bool_t PRunAsymmetry::PrepareFitData()
   Double_t asym;
   Double_t f, b, ef, eb;
   // fill data time start, and step
-  // data start at data_start-t0 shifted by (pack-1)/2
+  // data start time = (binStart - 0.5) + pack/2 - t0, with pack and binStart used as double
-  fData.SetDataTimeStart(fTimeResolution*(static_cast<Double_t>(fGoodBins[0])-fT0s[0]+static_cast<Double_t>(fPacking-1)/2.0));
+  fData.SetDataTimeStart(fTimeResolution*((static_cast<Double_t>(fGoodBins[0])-0.5) + static_cast<Double_t>(fPacking)/2.0 - static_cast<Double_t>(fT0s[0])));
   fData.SetDataTimeStep(fTimeResolution*static_cast<Double_t>(fPacking));
   for (UInt_t i=0; i<noOfBins; i++) {
     // to make the formulae more readable
@@ -1207,8 +1215,8 @@ Bool_t PRunAsymmetry::PrepareViewData(PRawRunData* runData, UInt_t histoNo[2])
   Double_t asym;
   Double_t f, b, ef, eb, alpha = 1.0, beta = 1.0;
   // set data time start, and step
-  // data start at data_start-t0
+  // data start time = (binStart - 0.5) + pack/2 - t0, with pack and binStart used as double
-  fData.SetDataTimeStart(fTimeResolution*(static_cast<Double_t>(start[0])-t0[0]+static_cast<Double_t>(packing-1)/2.0));
+  fData.SetDataTimeStart(fTimeResolution*((static_cast<Double_t>(start[0])-0.5) + static_cast<Double_t>(packing)/2.0 - static_cast<Double_t>(t0[0])));
   fData.SetDataTimeStep(fTimeResolution*static_cast<Double_t>(packing));
 
   // get the proper alpha and beta
@@ -1586,8 +1594,8 @@ Bool_t PRunAsymmetry::PrepareRRFViewData(PRawRunData* runData, UInt_t histoNo[2]
   }
 
   // set data time start, and step
-  // data start at data_start-t0
+  // data start time = (binStart - 0.5) + pack/2 - t0, with pack and binStart used as double
-  fData.SetDataTimeStart(fTimeResolution*(start[0]-t0[0]+static_cast<Double_t>(packing-1)/2.0));
+  fData.SetDataTimeStart(fTimeResolution*((static_cast<Double_t>(start[0])-0.5) + static_cast<Double_t>(packing)/2.0 - static_cast<Double_t>(t0[0])));
   fData.SetDataTimeStep(fTimeResolution*static_cast<Double_t>(packing));
 
   // ------------------------------------------------------------
@@ -1663,7 +1671,7 @@ Bool_t PRunAsymmetry::PrepareRRFViewData(PRawRunData* runData, UInt_t histoNo[2]
 //--------------------------------------------------------------------------
 /**
  * <p>Get the proper t0 for the single histogram run.
- * -# the t0 vector size = number of detectors (grouping) for forward.
+ * -# the t0 vector size = number of detectors (grouping) for forward + backward.
  * -# initialize t0's with -1
  * -# fill t0's from RUN block
  * -# if t0's are missing (i.e. t0 == -1), try to fill from the GLOBAL block.
@@ -1684,7 +1692,11 @@ Bool_t PRunAsymmetry::GetProperT0(PRawRunData* runData, PMsrGlobalBlock *globalB
   // feed all T0's
   // first init T0's, T0's are stored as (forward T0, backward T0, etc.)
   fT0s.clear();
-  fT0s.resize(2*forwardHistoNo.size());
+  // this strange fT0 size estimate is needed in case #forw histos != #back histos
+  size_t size = 2*forwardHistoNo.size();
+  if (backwardHistoNo.size() > forwardHistoNo.size())
+    size = 2*backwardHistoNo.size();
+  fT0s.resize(size);
   for (UInt_t i=0; i<fT0s.size(); i++) {
     fT0s[i] = -1.0;
   }
@@ -1751,6 +1763,8 @@ Bool_t PRunAsymmetry::GetProperT0(PRawRunData* runData, PMsrGlobalBlock *globalB
       std::cerr << std::endl;
       return false;
     }
+  }
+  for (UInt_t i=0; i<backwardHistoNo.size(); i++) {
     if ((fT0s[2*i+1] < 0) || (fT0s[2*i+1] > static_cast<Int_t>(runData->GetDataBin(backwardHistoNo[i])->size()))) {
       std::cerr << std::endl << ">> PRunAsymmetry::PrepareData(): **ERROR** t0 data bin (" << fT0s[2*i+1] << ") doesn't make any sense!";
       std::cerr << std::endl << ">> backwardHistoNo " << backwardHistoNo[i];

src/classes/PRunAsymmetryBNMR.cpp

@@ -640,6 +640,7 @@ Bool_t PRunAsymmetryBNMR::PrepareData()
       return false;
     }
   }
+/* //as35
   if (forwardHistoNo.size() != backwardHistoNo.size()) {
     std::cerr << std::endl << ">> PRunAsymmetryBNMR::PrepareData(): **PANIC ERROR**:";
     std::cerr << std::endl << ">> # of forward histograms different from # of backward histograms.";
@@ -650,6 +651,7 @@ Bool_t PRunAsymmetryBNMR::PrepareData()
     backwardHistoNo.clear();
     return false;
   }
+*/ //as35
   
   // keep the time resolution in (s)
   fTimeResolution = runData->GetTimeResolution()/1.0e3;
@@ -664,11 +666,13 @@ Bool_t PRunAsymmetryBNMR::PrepareData()
   // keep the histo of each group at this point (addruns handled below)
   std::vector<PDoubleVector> forward, backward;
   forward.resize(forwardHistoNo.size());   // resize to number of groups
-  backward.resize(backwardHistoNo.size()); // resize to numer of groups
   for (UInt_t i=0; i<forwardHistoNo.size(); i++) {
     forward[i].resize(runData->GetDataBin(forwardHistoNo[i])->size());
-    backward[i].resize(runData->GetDataBin(backwardHistoNo[i])->size());
     forward[i]  = *runData->GetDataBin(forwardHistoNo[i]);
+  }
+  backward.resize(backwardHistoNo.size()); // resize to number of groups
+  for (UInt_t i=0; i<backwardHistoNo.size(); i++) {
+    backward[i].resize(runData->GetDataBin(backwardHistoNo[i])->size());
     backward[i] = *runData->GetDataBin(backwardHistoNo[i]);
   }
 
@@ -712,15 +716,18 @@ Bool_t PRunAsymmetryBNMR::PrepareData()
     }
   }
 
-  // set forward/backward histo data of the first group
+  // set forward histo data of the first group
   fForwardp.resize(forward[0].size());
-  fBackwardp.resize(backward[0].size());
   fForwardm.resize(forward[0].size());
-  fBackwardm.resize(backward[0].size());
   for (UInt_t i=0; i<fForwardp.size(); i++) {
     fForwardp[i]  = forward[0][i];
-    fBackwardp[i] = backward[0][i];
     fForwardm[i]  = forward[1][i];
+  }
+  // set backward histo data of the first group
+  fBackwardp.resize(backward[0].size());
+  fBackwardm.resize(backward[0].size());
+  for (UInt_t i=0; i<fBackwardp.size(); i++) {
+    fBackwardp[i] = backward[0][i];
     fBackwardm[i] = backward[1][i];
   }
 
@@ -1529,7 +1536,11 @@ Bool_t PRunAsymmetryBNMR::GetProperT0(PRawRunData* runData, PMsrGlobalBlock *glo
   // feed all T0's
   // first init T0's, T0's are stored as (forward T0, backward T0, etc.)
   fT0s.clear();
-  fT0s.resize(2*forwardHistoNo.size());
+  // this strange fT0 size estimate is needed in case #forw histos != #back histos
+  size_t size = 2*forwardHistoNo.size();
+  if (backwardHistoNo.size() > forwardHistoNo.size())
+    size = 2*backwardHistoNo.size();
+  fT0s.resize(size);
   for (UInt_t i=0; i<fT0s.size(); i++) {
     fT0s[i] = -1.0;
   }
@@ -1596,6 +1607,8 @@ Bool_t PRunAsymmetryBNMR::GetProperT0(PRawRunData* runData, PMsrGlobalBlock *glo
       std::cerr << std::endl;
       return false;
     }
+  }
+  for (UInt_t i=0; i<backwardHistoNo.size(); i++) {
     if ((fT0s[2*i+1] < 0) || (fT0s[2*i+1] > static_cast<Int_t>(runData->GetDataBin(backwardHistoNo[i])->size()))) {
       std::cerr << std::endl << ">> PRunAsymmetryBNMR::PrepareData(): **ERROR** t0 data bin (" << fT0s[2*i+1] << ") doesn't make any sense!";
       std::cerr << std::endl << ">> backwardHistoNo " << backwardHistoNo[i];

src/classes/PRunAsymmetryRRF.cpp

@@ -584,16 +584,6 @@ Bool_t PRunAsymmetryRRF::PrepareData()
       return false;
     }
   }
-  if (forwardHistoNo.size() != backwardHistoNo.size()) {
-    std::cerr << std::endl << ">> PRunAsymmetryRRF::PrepareData(): **PANIC ERROR**:";
-    std::cerr << std::endl << ">> # of forward histograms different from # of backward histograms.";
-    std::cerr << std::endl << ">> Will quit :-(";
-    std::cerr << std::endl;
-    // clean up
-    forwardHistoNo.clear();
-    backwardHistoNo.clear();
-    return false;
-  }
 
   // keep the time resolution in (us)
   fTimeResolution = runData->GetTimeResolution()/1.0e3;
@@ -608,11 +598,13 @@ Bool_t PRunAsymmetryRRF::PrepareData()
   // keep the histo of each group at this point (addruns handled below)
   std::vector<PDoubleVector> forward, backward;
   forward.resize(forwardHistoNo.size());   // resize to number of groups
-  backward.resize(backwardHistoNo.size()); // resize to numer of groups
   for (UInt_t i=0; i<forwardHistoNo.size(); i++) {
     forward[i].resize(runData->GetDataBin(forwardHistoNo[i])->size());
-    backward[i].resize(runData->GetDataBin(backwardHistoNo[i])->size());
     forward[i]  = *runData->GetDataBin(forwardHistoNo[i]);
+  }
+  backward.resize(backwardHistoNo.size()); // resize to number of groups
+  for (UInt_t i=0; i<backwardHistoNo.size(); i++) {
+    backward[i].resize(runData->GetDataBin(backwardHistoNo[i])->size());
     backward[i] = *runData->GetDataBin(backwardHistoNo[i]);
   }
 
@@ -1281,7 +1273,11 @@ Bool_t PRunAsymmetryRRF::GetProperT0(PRawRunData* runData, PMsrGlobalBlock *glob
   // feed all T0's
   // first init T0's, T0's are stored as (forward T0, backward T0, etc.)
   fT0s.clear();
-  fT0s.resize(2*forwardHistoNo.size());
+  // this strange fT0 size estimate is needed in case #forw histos != #back histos
+  size_t size = 2*forwardHistoNo.size();
+  if (backwardHistoNo.size() > forwardHistoNo.size())
+    size = 2*backwardHistoNo.size();
+  fT0s.resize(size);
   for (UInt_t i=0; i<fT0s.size(); i++) {
     fT0s[i] = -1.0;
   }
@@ -1348,6 +1344,8 @@ Bool_t PRunAsymmetryRRF::GetProperT0(PRawRunData* runData, PMsrGlobalBlock *glob
       std::cerr << std::endl;
       return false;
     }
+  }
+  for (UInt_t i=0; i<backwardHistoNo.size(); i++) {
     if ((fT0s[2*i+1] < 0) || (fT0s[2*i+1] > static_cast<Int_t>(runData->GetDataBin(backwardHistoNo[i])->size()))) {
       std::cerr << std::endl << ">> PRunAsymmetryRRF::PrepareData(): **ERROR** t0 data bin (" << fT0s[2*i+1] << ") doesn't make any sense!";
       std::cerr << std::endl << ">> backwardHistoNo " << backwardHistoNo[i];

src/classes/PRunMuMinus.cpp

@@ -604,8 +604,8 @@ Bool_t PRunMuMinus::PrepareFitData(PRawRunData* runData, const UInt_t histoNo)
   Int_t t0 = static_cast<Int_t>(fT0s[0]);
   Double_t value = 0.0;
   // data start at data_start-t0
-  // time shifted so that packing is included correctly, i.e. t0 == t0 after packing
+  // data start time = (binStart - 0.5) + pack/2 - t0, with pack and binStart used as double
-  fData.SetDataTimeStart(fTimeResolution*(static_cast<Double_t>(fGoodBins[0])-static_cast<Double_t>(t0)+static_cast<Double_t>(fPacking-1)/2.0));
+  fData.SetDataTimeStart(fTimeResolution*((static_cast<Double_t>(fGoodBins[0])-0.5) + static_cast<Double_t>(fPacking)/2.0 - static_cast<Double_t>(t0)));
   fData.SetDataTimeStep(fTimeResolution*fPacking);
   for (Int_t i=fGoodBins[0]; i<fGoodBins[1]; i++) {
     if (fPacking == 1) {
@@ -710,9 +710,8 @@ Bool_t PRunMuMinus::PrepareRawViewData(PRawRunData* runData, const UInt_t histoN
   // everything looks fine, hence fill data set
   Int_t t0 = static_cast<Int_t>(fT0s[0]);
   Double_t value = 0.0;
-  // data start at data_start-t0
+  // data start time = (binStart - 0.5) + pack/2 - t0, with pack and binStart used as double
-  // time shifted so that packing is included correctly, i.e. t0 == t0 after packing
+  fData.SetDataTimeStart(fTimeResolution*((static_cast<Double_t>(start)-0.5) + static_cast<Double_t>(packing)/2.0 - static_cast<Double_t>(t0)));
-  fData.SetDataTimeStart(fTimeResolution*(static_cast<Double_t>(start)-static_cast<Double_t>(t0)+static_cast<Double_t>(packing-1)/2.0));
   fData.SetDataTimeStep(fTimeResolution*packing);
 
   for (Int_t i=start; i<end; i++) {

src/classes/PRunSingleHisto.cpp

@@ -888,7 +888,7 @@ Bool_t PRunSingleHisto::PrepareFitData(PRawRunData* runData, const UInt_t histoN
     normalizer = fPacking * (fTimeResolution * 1.0e3); // fTimeResolution us->ns
   // data start at data_start-t0
   // time shifted so that packing is included correctly, i.e. t0 == t0 after packing
-  fData.SetDataTimeStart(fTimeResolution*(static_cast<Double_t>(fGoodBins[0])-static_cast<Double_t>(t0)+static_cast<Double_t>(fPacking-1)/2.0));
+  fData.SetDataTimeStart(fTimeResolution*((static_cast<Double_t>(fGoodBins[0])-0.5) + static_cast<Double_t>(fPacking)/2.0 - static_cast<Double_t>(t0)));
   fData.SetDataTimeStep(fTimeResolution*fPacking);
   for (Int_t i=fGoodBins[0]; i<fGoodBins[1]; i++) {
     if (fPacking == 1) {
@@ -991,9 +991,8 @@ Bool_t PRunSingleHisto::PrepareRawViewData(PRawRunData* runData, const UInt_t hi
   // everything looks fine, hence fill data set
   Int_t t0 = static_cast<Int_t>(fT0s[0]);
   Double_t value = 0.0;
-  // data start at data_start-t0
+  // data start time = (binStart - 0.5) + pack/2 - t0, with pack and binStart used as double
-  // time shifted so that packing is included correctly, i.e. t0 == t0 after packing
+  fData.SetDataTimeStart(fTimeResolution*((static_cast<Double_t>(start)-0.5) + static_cast<Double_t>(packing)/2.0 - static_cast<Double_t>(t0)));
-  fData.SetDataTimeStart(fTimeResolution*(static_cast<Double_t>(start)-static_cast<Double_t>(t0)+static_cast<Double_t>(packing-1)/2.0));
   fData.SetDataTimeStep(fTimeResolution*packing);
 
   for (Int_t i=start; i<end; i++) {
@@ -1247,8 +1246,8 @@ Bool_t PRunSingleHisto::PrepareViewData(PRawRunData* runData, const UInt_t histo
   Double_t rrf_val = 0.0;
   Double_t time = 0.0;
 
-  // data start at data_start-t0 shifted by (pack-1)/2
+  // data start time = (binStart - 0.5) + pack/2 - t0, with pack and binStart used as double
-  fData.SetDataTimeStart(fTimeResolution*(static_cast<Double_t>(start)-static_cast<Double_t>(t0)+static_cast<Double_t>(packing-1)/2.0));
+  fData.SetDataTimeStart(fTimeResolution*((static_cast<Double_t>(start)-0.5) + static_cast<Double_t>(packing)/2.0 - static_cast<Double_t>(t0)));
   fData.SetDataTimeStep(fTimeResolution*packing);
 
   // data is always normalized to (per nsec!!)
@@ -1257,7 +1256,8 @@ Bool_t PRunSingleHisto::PrepareViewData(PRawRunData* runData, const UInt_t histo
     for (Int_t i=start; i<end; i++) {
       if (((i-start) % packing == 0) && (i != start)) { // fill data
         value *= dataNorm;
-        time = ((static_cast<Double_t>(i)-static_cast<Double_t>(packing-1)/2.0)-t0)*fTimeResolution;
+        // since the packing counter is already at the end of the bin, the time needs be shifted back by pack*time_resolution
+        time = (((static_cast<Double_t>(i)-0.5) + static_cast<Double_t>(packing)/2.0 - static_cast<Double_t>(t0)))*fTimeResolution - static_cast<Double_t>(packing)*fTimeResolution;
         expval = TMath::Exp(+time/tau)/N0;
         fData.AppendValue(-1.0+expval*(value-bkg));
         fData.AppendErrorValue(expval*TMath::Sqrt(value*dataNorm));
@@ -1316,7 +1316,7 @@ Bool_t PRunSingleHisto::PrepareViewData(PRawRunData* runData, const UInt_t histo
   // calculate theory
   Double_t theoryValue;
   UInt_t size = fForward.size()/packing;
-  Int_t factor = 8; // 8 times more points for the theory (if fTheoAsData == false)
+  const Int_t factor = 8; // 8 times more points for the theory (if fTheoAsData == false)
   UInt_t rebinRRF = 0;
 
   if (wRRF == 0) { // no RRF

src/dump_header.cpp

@@ -447,7 +447,8 @@ int dump_header_mud(const std::string fileName, const std::string fileFormat)
   // start time
   time_t tval;
   struct tm *dt;
-  success = MUD_getTimeBegin( fh, (UINT32*)&tval );
+  success = MUD_getTimeBegin( fh, &val );
+  tval = static_cast<time_t>(val);
   if (success) {
     dt = localtime(static_cast<const time_t*>(&tval));
     assert(dt);
@@ -457,7 +458,8 @@ int dump_header_mud(const std::string fileName, const std::string fileFormat)
     std::cout << std::endl << "Run Start Time     : ???";
   }
   // stop time
-  success = MUD_getTimeEnd( fh, (UINT32*)&tval );
+  success = MUD_getTimeEnd( fh, &val );
+  tval = static_cast<time_t>(val);
   if (success) {
     dt = localtime(static_cast<const time_t*>(&tval));
     assert(dt);

src/external/mud/src/mud.c

@@ -422,9 +422,7 @@ MUD_read( FILE* fin, MUD_IO_OPT io_opt )
      */	  
     if( ( pos = ftell( fin ) ) == EOF ) return( NULL );
     if( fread( &size, 4, 1, fin ) == 0 ) return( NULL );
-#if !defined(__arm64)
     bdecode_4( &size, &size );    /* byte ordering !!! */
-#endif // !defined(__arm64)
     if( fseek( fin, pos, 0 ) == EOF ) return( NULL );
 
 #ifdef DEBUG

src/external/nexus/PNeXus.cpp

@@ -818,10 +818,10 @@ PNeXusDetector2::PNeXusDetector2()
   fNoOfBins = -1;
 
   fT0Tag = -1;
-  fT0 = 0;
+  fT0 = nullptr;
-  fFirstGoodBin = 0;
+  fFirstGoodBin = nullptr;
-  fLastGoodBin = 0;
+  fLastGoodBin = nullptr;
-  fHisto = 0;
+  fHisto = nullptr;
 }
 
 //------------------------------------------------------------------------------------------
@@ -837,19 +837,19 @@ PNeXusDetector2::~PNeXusDetector2()
 
   if (fT0) {
     delete [] fT0;
-    fT0 = 0;
+    fT0 = nullptr;
   }
   if (fFirstGoodBin) {
     delete [] fFirstGoodBin;
-    fFirstGoodBin = 0;
+    fFirstGoodBin = nullptr;
   }
   if (fLastGoodBin) {
     delete [] fLastGoodBin;
-    fLastGoodBin = 0;
+    fLastGoodBin = nullptr;
   }
   if (fHisto) {
     delete [] fHisto;
-    fHisto = 0;
+    fHisto = nullptr;
   }
 }
 
@@ -921,8 +921,14 @@ int PNeXusDetector2::GetT0(int idxp, int idxs)
 {
   int result = -1;  
 
+  if (fT0Tag == 1) { // there is only ONE t0 present
+    if (fT0 != nullptr)
+      result = *fT0;
+    return result;
+  }
+
   if ((idxp < 0) && (idxs < 0)) { // assumption: there is only ONE t0 for all spectra
-    if (fT0 != 0) {
+    if (fT0 != nullptr) {
       result = *fT0;
     }
   } else if ((idxp < 0) && (idxs >= 0)) { // assumption: t0's are represented as t0[ns]
@@ -1031,16 +1037,23 @@ int PNeXusDetector2::GetFirstGoodBin(int idxp, int idxs)
 {
   int result = -1;
 
+  if (fT0Tag == 1) { // there is only ONE t0 present
+    if (fT0 != nullptr)
+      result = *fFirstGoodBin;
+    return result;
+  }
+
   if ((idxp < 0) && (idxs < 0)) { // assumption: there is only ONE t0 for all spectra
-    if (fFirstGoodBin != 0) {
+    if (fFirstGoodBin != nullptr) {
       result = *fFirstGoodBin;
     }
   } else if ((idxp < 0) && (idxs >= 0)) { // assumptions: fgb's are represented as fgb[ns]
-    if (idxs < fNoOfSpectra) {
+    if ((idxs < fNoOfSpectra) && (fFirstGoodBin != nullptr)) {
       result = *(fFirstGoodBin+idxs);
     }
   } else if ((idxp >= 0) && (idxs >= 0)) { // assumption: fgb's are represented as fgb[np][ns]
     if ((idxp < fNoOfPeriods) || (idxs < fNoOfSpectra)) {
+      if (fFirstGoodBin != nullptr)
         result = *(fFirstGoodBin+idxp*fNoOfSpectra+idxs);
     }
   } else {
@@ -1141,16 +1154,23 @@ int PNeXusDetector2::GetLastGoodBin(int idxp, int idxs)
 {
   int result = -1;
 
+  if (fT0Tag == 1) { // there is only ONE t0 present
+    if (fT0 != nullptr)
+      result = *fLastGoodBin;
+    return result;
+  }
+
   if ((idxp < 0) && (idxs < 0)) { // assumption: there is only ONE t0 for all spectra
-    if (fLastGoodBin != 0) {
+    if (fLastGoodBin != nullptr) {
       result = *fLastGoodBin;
     }
   } else if ((idxp < 0) && (idxs >= 0)) { // assumption: lgb's are represented as lgb[ns]
-    if (idxs < fNoOfSpectra) {
+    if ((idxs < fNoOfSpectra) && (fLastGoodBin != nullptr)) {
       result = *(fLastGoodBin+idxs);
     }
   } else if ((idxp >= 0) && (idxs >= 0)) { // assumption: lgb's are represented as lgb[np][ns]
     if ((idxp < fNoOfPeriods) || (idxs < fNoOfSpectra)) {
+      if (fLastGoodBin != nullptr)
         result = *(fLastGoodBin+idxp*fNoOfSpectra+idxs);
     }
   } else {
@@ -3398,6 +3418,14 @@ int PNeXus::ReadFileIdf2()
     return NX_ERROR;
   }
 
+  // beamline
+  if (SearchInGroup("beamline", "name", nxname, nxclass, dataType)) {
+    if (!ErrorHandler(NXopendata(fFileHandle, "beamline"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'beamline' data in NXentry!")) return NX_ERROR;
+    if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'beamline' data in NXentry!")) return NX_ERROR;
+    if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'beamline' data in NXentry!")) return NX_ERROR;
+    fNxEntry2->GetInstrument()->GetBeamline()->SetName(str);
+  }
+
   // definition
   if (!ErrorHandler(NXopendata(fFileHandle, "definition"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'definition' data in NXentry!")) return NX_ERROR;
   if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'definition' data in NXentry!")) return NX_ERROR;
@@ -3576,7 +3604,9 @@ int PNeXus::ReadFileIdf2()
   // close group NXsource
   NXclosegroup(fFileHandle);
 
+
   // open group NXbeamline
+  if (SearchInGroup("beamline", "name", nxname, nxclass, dataType)) {
     if (!ErrorHandler(NXopengroup(fFileHandle, "beamline", "NXbeamline"), PNEXUS_GROUP_OPEN_ERROR, "couldn't open NeXus subgroup beamline in NXinstrument!")) return NX_ERROR;
 
     // beamline name
@@ -3587,15 +3617,24 @@ int PNeXus::ReadFileIdf2()
 
     // close group NXbeamline
     NXclosegroup(fFileHandle);
+  } else {
+    std::cerr << "**WARNING** in class NXinstrument the object NXbeamline with name 'beamline' is missing!" << std::endl;
+    std::cerr << "            Complain at the facility where you got this data file from!" << std::endl;
+  }
 
-  // open group NXdetector
+  // open group NXdetector in instrument (NXinstrument)
   if (!ErrorHandler(NXopengroup(fFileHandle, "detector_1", "NXdetector"), PNEXUS_GROUP_OPEN_ERROR, "couldn't open NeXus subgroup detector_1 in NXinstrument!")) return NX_ERROR;
 
   // description
+  if (SearchInGroup("description", "name", nxname, nxclass, dataType)) {
     if (!ErrorHandler(NXopendata(fFileHandle, "description"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'description' data in NXdetector!")) return NX_ERROR;
     if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'description' data in NXdetector!")) return NX_ERROR;
     if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'description' data in NXdetector!")) return NX_ERROR;
     fNxEntry2->GetInstrument()->GetDetector()->SetDescription(str);
+  } else {
+    std::cerr << "**WARNING** in class NXdetector to object NX_CHAR with name 'description' is missing!" << std::endl;
+    std::cerr << "            Complain at the facility where you got this data file from!" << std::endl;
+  }
 
   // get the time resolution. This is a little bit complicated since it is either present as 'histogram_resolution' or needs to be extracted from the 'raw_time' vector
   // 1st check if 'histogram_resolution' is found
@@ -3607,10 +3646,10 @@ int PNeXus::ReadFileIdf2()
     fNxEntry2->GetInstrument()->GetDetector()->SetTimeResolution((double)fval, str);
   } else if (SearchInGroup("resolution", "name", nxname, nxclass, dataType)) { // 2nd check if 'resolution' is found
     if (!ErrorHandler(NXopendata(fFileHandle, "resolution"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'resolution' data in NXdetector!")) return NX_ERROR;
-    if (!ErrorHandler(NXgetdata(fFileHandle, &fval), PNEXUS_GET_DATA_ERROR, "couldn't read 'resolution' data in NXdetector!")) return NX_ERROR;
+    if (!ErrorHandler(NXgetdata(fFileHandle, &ival), PNEXUS_GET_DATA_ERROR, "couldn't read 'resolution' data in NXdetector!")) return NX_ERROR;
     if (!ErrorHandler(GetStringAttr("units", str), PNEXUS_GET_ATTR_ERROR, "couldn't read time resolution units in NXdetector!")) return NX_ERROR;
     if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'resolution' data in NXdetector!")) return NX_ERROR;
-    fNxEntry2->GetInstrument()->GetDetector()->SetTimeResolution((double)fval, str);
+    fNxEntry2->GetInstrument()->GetDetector()->SetTimeResolution((double)ival, str);
   } else { // 3nd 'histogram_resolution' is not present, hence extract the time resolution from the 'raw_time' vector
     if (!ErrorHandler(NXopendata(fFileHandle, "raw_time"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'raw_time' data in NXdetector!")) return NX_ERROR;
     std::vector<double> rawTime;
@@ -3626,6 +3665,51 @@ int PNeXus::ReadFileIdf2()
   // check the dimensions of 'counts'
   if (!ErrorHandler(NXgetinfo(fFileHandle, &rank, dims, &type), PNEXUS_GET_META_INFO_ERROR, "couldn't get 'counts' info in NXdetector!")) return NX_ERROR;
 
+  // check if last_good_bin, first_good_bin, and t0_bins are defined as attributes
+  int attLen = 1, attType = NX_INT32;
+  if (SearchAttrInData("first_good_bin", attLen, attType)) {
+    char  cstr[1204];
+    memset(cstr, '\0', sizeof(cstr));
+    strncpy(cstr, "first_good_bin", sizeof(cstr));
+    status = NXgetattr(fFileHandle, cstr, (void*)&ival, &attLen, &attType);
+
+    fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(1); // a single set for t0, fgb, lgb is likely given
+    int *i_data_ptr = new int;
+    *i_data_ptr = ival;
+    if (!fNxEntry2->GetInstrument()->GetDetector()->SetFirstGoodBin(i_data_ptr)) {
+      std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
+      return NX_ERROR;
+    }
+  }
+  if (SearchAttrInData("last_good_bin", attLen, attType)) {
+    char  cstr[1204];
+    memset(cstr, '\0', sizeof(cstr));
+    strncpy(cstr, "last_good_bin", sizeof(cstr));
+    status = NXgetattr(fFileHandle, cstr, (void*)&ival, &attLen, &attType);
+
+    fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(1); // a single set for t0, fgb, lgb is likely given
+    int *i_data_ptr = new int;
+    *i_data_ptr = ival;
+    if (!fNxEntry2->GetInstrument()->GetDetector()->SetLastGoodBin(i_data_ptr)) {
+      std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
+      return NX_ERROR;
+    }
+  }
+  if (SearchAttrInData("t0_bin", attLen, attType)) {
+    char  cstr[1204];
+    memset(cstr, '\0', sizeof(cstr));
+    strncpy(cstr, "t0_bin", sizeof(cstr));
+    status = NXgetattr(fFileHandle, cstr, (void*)&ival, &attLen, &attType);
+
+    fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(1); // a single set for t0, fgb, lgb is likely given
+    int *i_data_ptr = new int;
+    *i_data_ptr = ival;
+    if (!fNxEntry2->GetInstrument()->GetDetector()->SetT0(i_data_ptr)) {
+      std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
+      return NX_ERROR;
+    }
+  }
+
   // calculate the needed size
   size = dims[0];
   for (int i=1; i<rank; i++)
@@ -3713,6 +3797,8 @@ int PNeXus::ReadFileIdf2()
 
   if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'spectrum_index' data in NXdetector!")) return NX_ERROR;
 
+  // only handle t0, fgb, lgb, if they are not already set as an attribute of /raw_data_1/instrument/detector_1/counts
+  if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == -1) {
     // handle t0's
     if (SearchInGroup("time_zero_bin", "name", nxname, nxclass, dataType)) { // check for 'time_zero_bin'
       if (!ErrorHandler(NXopendata(fFileHandle, "time_zero_bin"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'time_zero_bin' data in NXdetector!")) return NX_ERROR;
@@ -4028,6 +4114,7 @@ int PNeXus::ReadFileIdf2()
     } else {
       std::cerr << std::endl << ">> **WARNING** found neither 'last_good_bin' nor 'last_good_time' values ..." << std::endl;
     }
+  }
 
   // close group NXdetector
   NXclosegroup(fFileHandle);