start working on the deadtime correction.

doc/examples/test-histo-NeXus2.msr

@@ -3,21 +3,20 @@ Ag_T=100_F=20
 FITPARAMETER
 #       No Name        Value     Step        Pos_Error   Boundaries
         1 zero        0         0           none        
-        2 phase       0.00000000029  -0.00000000029 0.00985861603 0       100     
+        2 phase       0.000000011  -0.000000011 0.005772888 0       100     
-        3 field       20.3708   -0.0088     0.0088      0       none    
+        3 field       20.3391   -0.0085     0.0085      0       none    
-        4 asym        0.23135   -0.00065    0.00066     0       0.3     
+        4 asym        0.23461   -0.00051    0.00051     0       0.3     
-        5 rate        0.0074    0.0049      none        0       100     
+        5 rate        0.0239    -0.0040     0.0035      0       100     
-        6 beta        1.867     0.043       none        
+        6 Norm_L      1151.24   -0.53       0.53        
-        7 Norm_L      1135.66   -0.58       0.58        
+        7 BG_L        0         0           none        0       none    
-        8 BG_L        0         0           none        0       none    
+        8 Norm_R      1178.60   -0.58       0.58        0       none    
-        9 Norm_R      1168.88   -0.61       0.61        0       none    
+        9 BG_R        0         0           none        0       none    
-       10 BG_R        0         0           none        0       none    
+       10 relPhase    178.49    -0.20       0.20        0       none    
-       11 relPhase    177.40    -0.20       0.21        0       none    
 
 ###############################################################
 THEORY
 asymmetry      4
-generExpo      5     6       (rate exponent)
+simpleGss      5          (rate)
 TFieldCos   fun1  fun2       (phase frequency)
 
 ###############################################################
@@ -28,21 +27,24 @@ fun2 = gamma_mu * par3
 ###############################################################
 GLOBAL
 fittype         0         (single histogram fit)
-data            10      2048    
+data            5       2048    
-fit             0.2     14     
+t0              10.0    
+deadtime-cor    file
+fit             0.144   30     
 packing         1
 
 ###############################################################
-RUN data/emu00139040 XXXX ISIS NEXUS   (name beamline institute data-file-format)
+RUN data/emu00139040 EMU ISIS NEXUS   (name beamline institute data-file-format)
-norm            7
+norm            6
-backgr.fit      8
+backgr.fit      7
 map             1    0    0    0    0    0    0    0    0    0
 forward         1-48 
+#deadtime-cor    file
 
 RUN data/emu00139040 XXXX ISIS NEXUS   (name beamline institute data-file-format)
-norm            9
+norm            8
-backgr.fit      10
+backgr.fit      9
-map            11    0    0    0    0    0    0    0    0    0
+map            10    0    0    0    0    0    0    0    0    0
 forward         49-96 
 
 ###############################################################
@@ -59,15 +61,15 @@ fourier_power    11
 apodization      STRONG  # NONE, WEAK, MEDIUM, STRONG
 plot             REAL    # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE, PHASE_OPT_REAL
 range            0    200
-phase            parR2, par11
+phase            parR2, par10
 
 ###############################################################
 PLOT 0   (single histo plot)
 lifetimecorrection
 runs        1   2
-range    0   14   -0.35   0.35
+range    0   20   -0.35   0.35
-view_packing 10
+#view_packing 10
 
 ###############################################################
-STATISTIC --- 2026-02-05 10:47:55
+STATISTIC --- 2026-02-08 15:32:12
-  maxLH = 2154.1, NDF = 1684, maxLH/NDF = 1.279168
+  maxLH = 4233.1, NDF = 3725, maxLH/NDF = 1.136412

src/classes/PMusr.cpp

@@ -721,6 +721,22 @@ PRawRunDataSet* PRawRunData::GetDataSet(const UInt_t idx, Bool_t wantHistoNo)
     return fData.GetSet(idx);
 }
 
+//--------------------------------------------------------------------------
+// DeadTimeCorrectionReady (public)
+//--------------------------------------------------------------------------
+/**
+ * <p>Checks if deadtime correction information is sufficient to apply it.
+ * This means that fNumberOfGoodFrames must be present and the deadtime
+ * parameter vector.
+ *
+ * @return true if ready to apply deadtime correctio, false otherwise
+ */
+const Bool_t PRawRunData::DeadTimeCorrectionReady()
+{
+  if ((fNumberOfGoodFrames > 0) && (fDeadTimeParam.size() > 0))
+    return true;
+  return false;
+}
 
 //--------------------------------------------------------------------------
 // SetRingAnode (public)

src/classes/PRunSingleHisto.cpp

@@ -1069,6 +1069,38 @@ Bool_t PRunSingleHisto::PrepareData()
     forward[i] = *runData->GetDataBin(histoNo[i]);
   }
 
+  // check if a dead time correction has to be done
+  // first check the global block
+  TString dtcg = fMsrInfo->GetMsrGlobal()->GetDeadTimeCorrection();
+  Int_t dtcg_tag = 0; // 0=no, 1=file, 2=estimate
+  if (dtcg.Contains("file", TString::kIgnoreCase)) {
+    dtcg_tag = 1;
+  } else if (dtcg.Contains("estimate", TString::kIgnoreCase)) {
+    dtcg_tag = 2;
+  }
+  // now check each run
+  TString dtcr{"no"};
+  Bool_t needToCheck{true};
+  for (UInt_t i=0; i<histoNo.size(); i++) {
+    dtcr = fRunInfo->GetDeadTimeCorrection();
+    if (dtcr.Contains("file", TString::kIgnoreCase) || (dtcg_tag != 0)) {
+      if (runData->DeadTimeCorrectionReady()) {
+        needToCheck = false;
+        // Dead time correction: n_true = n_obs / (1 - n_obs * t_dt / (good_frames * dt))
+        Double_t n_true;
+        Int_t gf = runData->GetNumberOfGoodFrames();
+        std::vector<float> t_dt = runData->GetDeadTimeParam();
+        for (UInt_t j=0; j<forward[i].size(); j++) {
+          n_true = forward[i][j] / (1.0 - forward[i][j] * t_dt[histoNo[i]] / (gf * fTimeResolution));
+          forward[i][j] = n_true;
+        }
+      }
+    }
+    if ((dtcr.Contains("estimate", TString::kIgnoreCase) || (dtcg_tag != 0)) && needToCheck) {
+      std::cerr << "as35> run: deadtime correction: " << dtcr.Data() << ", global: " << dtcg_tag << std::endl;
+    }
+  }
+
   // check if there are runs to be added to the current one
   if (fRunInfo->GetRunNameSize() > 1) { // runs to be added present
     PRawRunData *addRunData;

src/external/nexus/PNeXus.cpp

@@ -3744,7 +3744,7 @@ void nxH5::PNeXus::HandleIdfV2(H5::H5File &file)
     ReadIntDataset(file, "/raw_data_1/instrument/detector_1/counts");
     ReadFloatDataset(file, "/raw_data_1/instrument/detector_1/raw_time");
     ReadIntDataset(file, "/raw_data_1/instrument/detector_1/spectrum_index");
-    ReadFloatDataset(file, "/raw_data_1/detector_1/dead_time");
+    ReadFloatDataset(file, "/raw_data_1/instrument/detector_1/dead_time");
     ReadStringDataset(file, "/raw_data_1/sample/name");
     ReadFloatDataset(file, "/raw_data_1/sample/temperature");
     ReadFloatDataset(file, "/raw_data_1/sample/magnetic_field");
@@ -4739,7 +4739,7 @@ void nxH5::PNeXus::Dump()
     std::cout << std::endl << "  dead_time:";
     std::cout << std::endl;
     try {
-      auto dead_time = std::any_cast<PNXdata<float>>(fDataMap["/raw_data_1/detector_1/dead_time"]);
+      auto dead_time = std::any_cast<PNXdata<float>>(fDataMap["/raw_data_1/instrument/detector_1/dead_time"]);
       const auto& data = dead_time.GetData();
 
       // dump the first couple of raw_times

src/include/PMusr.h

@@ -872,6 +872,7 @@ class PRawRunData {
     virtual const PIntPair GetBkgBin(const UInt_t histoNo) { return fData.GetBkgBin(histoNo); }
     virtual const PIntPair GetGoodDataBin(const UInt_t histoNo) { return fData.GetGoodDataBin(histoNo); }
     virtual const PIntVector GetRedGreenOffset() { return fRedGreenOffset; }
+    virtual const Bool_t DeadTimeCorrectionReady();
     virtual const Int_t GetNumberOfGoodFrames() { return fNumberOfGoodFrames; }
     virtual const std::vector<float> GetDeadTimeParam() { return fDeadTimeParam; }
     virtual const UInt_t GetNoOfHistos() { return fData.Size(); }

src/include/PRunDataHandler.h

@@ -824,9 +824,9 @@ Bool_t PRunDataHandler::ReadNexusFileIdf2(T& nxs_file)
   }
 
   // get/set deadtime relevant parameters
-  if (nxs_file->HasDataset("/raw_data_1/instrument/detector1/dead_time")) {
+  if (nxs_file->HasDataset("/raw_data_1/instrument/detector_1/dead_time")) {
     std::vector<float> dt;
-    dt = nxs_file->template GetDataset<float>("/raw_data_1/instrument/detector1/dead_time").GetData();
+    dt = nxs_file->template GetDataset<float>("/raw_data_1/instrument/detector_1/dead_time").GetData();
     runData.SetDeadTimeParam(dt);
   }
   if (nxs_file->HasDataset("/raw_data_1/good_frames")) {