From 7b8574b3eef90d26c7656644a9aab486877cf39b Mon Sep 17 00:00:00 2001
From: Andreas Suter <andreas.suter@psi.ch>
Date: Tue, 13 Oct 2026 09:00:56 +0200
Subject: [PATCH] musrt0 -g: handle msr-files with a GLOBAL block.

If 't0' and/or 'addt0' is present in the GLOBAL block, only issue a warning and
leave the msr-file untouched. Otherwise the estimated t0's are added/updated in
the RUN blocks. Missing t0/addt0/background/data tags were only written at the
'fit' line of a RUN block, which is absent if the fit range is given in the
GLOBAL block; in this case they are now written after the last line of the RUN block.
---
 src/classes/PMsrHandler.cpp | 144 ++++++++++++++++++++++--------------
 src/musrt0.cpp              |  10 +++
 2 files changed, 99 insertions(+), 55 deletions(-)

diff --git a/src/classes/PMsrHandler.cpp b/src/classes/PMsrHandler.cpp
index 4c8b3cf3..5e1cce93 100644
--- a/src/classes/PMsrHandler.cpp
+++ b/src/classes/PMsrHandler.cpp
@@ -475,6 +475,15 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
   for (UInt_t i=0; i<fRuns.size(); i++) {
     dataTagMissing.push_back(true);
   }
+  // if the fit range is given in the GLOBAL block, the RUN block has no 'fit' line
+  // after which missing tags could be added. In this case they are added after the
+  // last non-empty line of the RUN block.
+  PBoolVector fitTagMissing; // needed for proper musrt0 handling
+  PIntVector lastRunLineNo;
+  for (UInt_t i=0; i<fRuns.size(); i++) {
+    fitTagMissing.push_back(true);
+    lastRunLineNo.push_back(-1);
+  }
 
   // add some counters needed in connection to addruns
   Int_t addT0Counter = 0;
@@ -489,19 +498,35 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
   if (!fin.is_open()) {
     return PMUSR_MSR_LOG_FILE_WRITE_ERROR;
   }
+  Bool_t inRunBlock = false;
+  lineNo = 0;
   while (!fin.eof()) {
     // read a line
     getline(fin, line);
     str = line.c_str();
+    lineNo++;
 
     if (str.BeginsWith("RUN")) {
       runNo++;
+      inRunBlock = true;
+      lastRunLineNo[runNo] = lineNo;
       continue;
     }
 
+    if (str.BeginsWith("FITPARAMETER") || str.BeginsWith("THEORY") || str.BeginsWith("FUNCTIONS") ||
+        str.BeginsWith("GLOBAL") || str.BeginsWith("COMMANDS") || str.BeginsWith("FOURIER") ||
+        str.BeginsWith("PLOT") || str.BeginsWith("STATISTIC"))
+      inRunBlock = false;
+
     if (runNo == -1)
       continue;
 
+    if (inRunBlock && !str.IsWhitespace() && !str.BeginsWith("#")) {
+      lastRunLineNo[runNo] = lineNo;
+      if (str.BeginsWith("fit") && !str.BeginsWith("fittype"))
+        fitTagMissing[runNo] = false;
+    }
+
     if (str.BeginsWith("t0"))
       t0TagMissing[runNo] = false;
     else if (str.BeginsWith("background"))
@@ -537,6 +562,65 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
     return PMUSR_MSR_LOG_FILE_WRITE_ERROR;
   }
 
+  // writes t0/addt0/background/data of a RUN block, if the corresponding tag is missing in the msr-file
+  auto writeMissingRunTags = [&](Int_t runNo) {
+    // if ISIS data, do not do anything
+    if (t0TagMissing[runNo] && fRuns[runNo].GetInstitute()->CompareTo("isis", TString::kIgnoreCase)) {
+      if (fRuns[runNo].GetT0BinSize() > 0) {
+        fout.width(16);
+        fout << std::left << "t0";
+        for (UInt_t j=0; j<fRuns[runNo].GetT0BinSize(); j++) {
+          fout.width(8);
+          fout.precision(1);
+          fout.setf(std::ios::fixed,std::ios::floatfield);
+          fout << std::left << fRuns[runNo].GetT0Bin(j);
+        }
+        fout << std::endl;
+      }
+    }
+    for (UInt_t i=0; i<fRuns[runNo].GetAddT0BinEntries(); i++) {
+      if (addt0TagMissing[runNo][i]  && fRuns[runNo].GetInstitute()->CompareTo("isis", TString::kIgnoreCase)) {
+        if (fRuns[runNo].GetAddT0BinSize(i) > 0) {
+          fout.width(16);
+          fout << std::left << "addt0";
+          for (Int_t j=0; j<fRuns[runNo].GetAddT0BinSize(i); j++) {
+            fout.width(8);
+            fout.precision(1);
+            fout.setf(std::ios::fixed,std::ios::floatfield);
+            fout << std::left << fRuns[runNo].GetAddT0Bin(i, j);
+          }
+          fout << std::endl;
+        }
+      }
+    }
+    if (backgroundTagMissing[runNo]) {
+      if (fRuns[runNo].GetBkgRange(0) >= 0) {
+        fout.width(16);
+        fout << std::left << "background";
+        for (UInt_t j=0; j<4; j++) {
+          if (fRuns[runNo].GetBkgRange(j) > 0) {
+            fout.width(8);
+            fout << std::left << fRuns[runNo].GetBkgRange(j);
+          }
+        }
+        fout << std::endl;
+      }
+    }
+    if (dataTagMissing[runNo]) {
+      if (fRuns[runNo].GetDataRange(0) >= 0) {
+        fout.width(16);
+        fout << std::left << "data";
+        for (UInt_t j=0; j<4; j++) {
+          if (fRuns[runNo].GetDataRange(j) > 0) {
+            fout.width(8);
+            fout << std::left << fRuns[runNo].GetDataRange(j);
+          }
+        }
+        fout << std::endl;
+      }
+    }
+  };
+
   tag = MSR_TAG_TITLE;
   lineNo = 0;
   runNo = -1;
@@ -1068,61 +1152,7 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
           }
         } else if (sstr.BeginsWith("fit")) {
           // check if missing t0/addt0/background/data tag are present eventhough the values are present, if so write these data values
-          // if ISIS data, do not do anything
-          if (t0TagMissing[runNo] && fRuns[runNo].GetInstitute()->CompareTo("isis", TString::kIgnoreCase)) {
-            if (fRuns[runNo].GetT0BinSize() > 0) {
-              fout.width(16);
-              fout << std::left << "t0";
-              for (UInt_t j=0; j<fRuns[runNo].GetT0BinSize(); j++) {
-                fout.width(8);
-                fout.precision(1);
-                fout.setf(std::ios::fixed,std::ios::floatfield);
-                fout << std::left << fRuns[runNo].GetT0Bin(j);
-              }
-              fout << std::endl;
-            }
-          }
-          for (UInt_t i=0; i<fRuns[runNo].GetAddT0BinEntries(); i++) {
-            if (addt0TagMissing[runNo][i]  && fRuns[runNo].GetInstitute()->CompareTo("isis", TString::kIgnoreCase)) {
-              if (fRuns[runNo].GetAddT0BinSize(i) > 0) {
-                fout.width(16);
-                fout << std::left << "addt0";
-                for (Int_t j=0; j<fRuns[runNo].GetAddT0BinSize(i); j++) {
-                  fout.width(8);
-                  fout.precision(1);
-                  fout.setf(std::ios::fixed,std::ios::floatfield);
-                  fout << std::left << fRuns[runNo].GetAddT0Bin(i, j);
-                }
-                fout << std::endl;
-              }
-            }
-          }
-          if (backgroundTagMissing[runNo]) {
-            if (fRuns[runNo].GetBkgRange(0) >= 0) {
-              fout.width(16);
-              fout << std::left << "background";
-              for (UInt_t j=0; j<4; j++) {
-                if (fRuns[runNo].GetBkgRange(j) > 0) {
-                  fout.width(8);
-                  fout << std::left << fRuns[runNo].GetBkgRange(j);
-                }
-              }
-              fout << std::endl;
-            }
-          }
-          if (dataTagMissing[runNo]) {
-            if (fRuns[runNo].GetDataRange(0) >= 0) {
-              fout.width(16);
-              fout << std::left << "data";
-              for (UInt_t j=0; j<4; j++) {
-                if (fRuns[runNo].GetDataRange(j) > 0) {
-                  fout.width(8);
-                  fout << std::left << fRuns[runNo].GetDataRange(j);
-                }
-              }
-              fout << std::endl;
-            }
-          }
+          writeMissingRunTags(runNo);
           // write fit range line
           fout.width(16);
           fout << std::left << "fit";
@@ -1163,6 +1193,10 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
         } else {
           fout << str.Data() << std::endl;
         }
+        // no 'fit' line in the RUN block (fit range given in the GLOBAL block), hence
+        // write missing tags after the last line of the RUN block
+        if (fitTagMissing[runNo] && (lineNo == lastRunLineNo[runNo]))
+          writeMissingRunTags(runNo);
         break;
       case MSR_TAG_COMMANDS:
         fout << str.Data() << std::endl;
diff --git a/src/musrt0.cpp b/src/musrt0.cpp
index 192f30d0..d8768350 100644
--- a/src/musrt0.cpp
+++ b/src/musrt0.cpp
@@ -346,6 +346,16 @@ Int_t main(Int_t argc, Char_t *argv[])
     }
   }
 
+  // t0's given in the GLOBAL block are not touched by the prompt peak estimate
+  if (getT0FromPromptPeak && success) {
+    PMsrGlobalBlock *global = msrHandler->GetMsrGlobal();
+    if ((global->GetT0BinSize() > 0) || (global->GetAddT0BinEntries() > 0)) {
+      std::cerr << std::endl << ">> musrt0 **WARNING** 't0' and/or 'addt0' already found in the GLOBAL block.";
+      std::cerr << std::endl << ">>   Will not estimate t0's from the prompt peak, the msr-file is left untouched." << std::endl << std::endl;
+      return PMUSR_SUCCESS;
+    }
+  }
+
   if (getT0FromPromptPeak && success) {
 
     Int_t  histoNo = -1;