start working on the deadtime correction.

Generate git-revision.h into CMAKE_BINARY_DIR/src/ (which is in the
include path) instead of the source tree. Remove the header from
add_executable() source lists, and add missing add_dependencies on
git_revision for all Qt5/Qt6 targets.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

CMakeLists.txt

@@ -6,7 +6,7 @@ if (CMAKE_VERSION GREATER_EQUAL "3.3")
   cmake_policy(SET CMP0167 NEW)
 endif ()  
 
-project(musrfit VERSION 1.9.10 LANGUAGES C CXX)
+project(musrfit VERSION 1.9.11 LANGUAGES C CXX)
 
 #--- musrfit specific options -------------------------------------------------
 option(nexus "build optional NeXus support. Needed for ISIS" OFF)
@@ -211,14 +211,41 @@ if (qt_based_tools)
   endif (qt_version STREQUAL 3)
 endif (qt_based_tools)
 
-#--- if NeXus check also for HDF4, HDF5, and MXML -----------------------------
+#--- if NeXus check also for HDF4 (optional), HDF5 ----------------------------
 if (nexus)
   find_package(HDF5 COMPONENTS CXX REQUIRED)
   if (HAVE_HDF4)
-    find_package(HDF4 REQUIRED)
+    #--- check for HDF4 -----------------------------------------------------------
+    # Find HDF4 manually (pkg-config often doesn't have hdf4)
+    find_path(HDF4_INCLUDE_DIR
+      NAMES mfhdf.h
+      PATHS /usr/include /usr/local/include
+      PATH_SUFFIXES hdf
+    )
+
+    find_library(HDF4_DF_LIBRARY
+      NAMES df libdf
+      PATHS /usr/lib64 /usr/lib /usr/local/lib64 /usr/local/lib
+    )
+
+    find_library(HDF4_MFHDF_LIBRARY
+      NAMES mfhdf libmfhdf
+      PATHS /usr/lib64 /usr/lib /usr/local/lib64 /usr/local/lib
+    )
+
+    if (HDF4_INCLUDE_DIR AND HDF4_DF_LIBRARY AND HDF4_MFHDF_LIBRARY)
+      set(HDF4_FOUND TRUE)
+      set(HDF4_INCLUDE_DIRS ${HDF4_INCLUDE_DIR})
+      set(HDF4_LIBRARIES ${HDF4_MFHDF_LIBRARY} ${HDF4_DF_LIBRARY})
+      message(STATUS "Found HDF4: ${HDF4_INCLUDE_DIR}")
+      message(STATUS "  HDF4 libraries: ${HDF4_LIBRARIES}")
+    else()
+      message(FATAL_ERROR "HDF4 library not found. Please install libhdf4-dev or hdf-devel")
+    endif()
+
+    include_directories(${HDF4_INCLUDE_DIRS})
     add_definitions(-DHAVE_HDF4)
   endif (HAVE_HDF4)  
-  find_package(NEXUS REQUIRED)
   add_definitions(-DPNEXUS_ENABLED)
 endif (nexus)
 
@@ -323,7 +350,6 @@ if (nexus)
     message(" HDF4    not present.")	  
   endif (HAVE_HDF4)	  
   message(" HDF5    found in ${HDF5_INCLUDE_DIRS}, Version: ${HDF5_VERSION}")
-  message(" NeXus   found in ${NEXUS_INCLUDE_DIR}, Version: ${NEXUS_VERSION_STRING}")
 endif (nexus)
 
 message("")

cmake/FindHDF4.cmake

@@ -1,97 +0,0 @@
-## Process this file with cmake
-#=============================================================================
-#  NeXus - Neutron & X-ray Common Data Format
-#
-#  CMakeLists for building the NeXus library and applications.
-#
-#  Copyright (C) 2011 Stephen Rankin
-#
-#  This library is free software; you can redistribute it and/or modify it
-#  under the terms of the GNU Lesser General Public License as published by the
-#  Free Software Foundation; either version 2 of the License, or (at your
-#  option) any later version.
-#
-#  This library is distributed in the hope that it will be useful, but WITHOUT
-#  ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-#  FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License
-#  for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public License
-#  along with this library; if not, write to the Free Software Foundation,
-#  Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-#
-#  For further information, see <http://www.nexusformat.org>
-#
-#
-#=============================================================================
-
-
-#------------------------------------------------------------------------------
-# find the runtime binaries of the HDF4 library
-#------------------------------------------------------------------------------
-find_library(HDF4_DF_LIBRARY NAMES df hdf
-             HINTS ENV HDF4_ROOT 
-             PATH_SUFFIXES hdf)
-             
-
-if(HDF4_DF_LIBRARY MATCHES HDF4_DF_LIBRARY-NOTFOUND)
-    message(FATAL_ERROR "Could not find HDF4 DF library!")
-else()
-    get_filename_component(HDF4_LIBRARY_DIRS ${HDF4_DF_LIBRARY} PATH)
-    message(STATUS "Found HDF4 DF library: ${HDF4_DF_LIBRARY}")
-    message(STATUS "HDF4 libary path: ${HDF4_LIBRARY_DIRS}")
-endif()
-
-find_library(HDF4_MFHDF_LIBRARY NAMES mfhdf 
-             HINTS ENV HDF4_ROOT
-             PATH_SUFFIXES hdf)
-
-if(HDF4_MFHDF_LIBRARY MATCHES HDF4_MFHDF_LIBRARY-NOTFOUND)
-    message(FATAL_ERROR "Could not find HDF5 MFHDF library!")
-else()
-    message(STATUS "Found HDF4 MFHDF library: ${HDF4_MFHDF_LIBRARY}")
-endif()
-
-
-#------------------------------------------------------------------------------
-# find the HDF4 header file
-#------------------------------------------------------------------------------
-find_path(HDF4_INCLUDE_DIRS mfhdf.h 
-          HINTS ENV HDF4_ROOT 
-          PATH_SUFFIXES hdf)
-          
-if(HDF4_INCLUDE_DIRS MATCHES HDF4_INCLUDE_DIRS-NOTFOUND)
-    message(FATAL_ERROR "Could not find HDF4 header files")
-else()
-    message(STATUS "Found HDF4 header files in: ${HDF4_INCLUDE_DIRS}")
-endif()
-
-#------------------------------------------------------------------------------
-# search for additional packages required to link against HDF4
-#------------------------------------------------------------------------------
-find_package(JPEG REQUIRED)
-
-#------------------------------------------------------------------------------
-# add libraries to the link list for NAPI
-#------------------------------------------------------------------------------
-get_filename_component(LIB_EXT ${HDF4_DF_LIBRARY} EXT)
-if(LIB_EXT MATCHES .a)
-    message(STATUS "HDF4 DF library is static")
-    list(APPEND NAPI_LINK_LIBS "-Wl,-whole-archive" ${HDF4_DF_LIBRARY} "-Wl,-no-whole-archive")
-else()
-    list(APPEND NAPI_LINK_LIBS ${HDF4_DF_LIBRARY})
-endif()
-
-
-get_filename_component(LIB_EXT ${HDF4_MFHDF_LIBRARY} EXT)
-if(LIB_EXT MATCHES .a)
-    message(STATUS "HDF4 MFHDF library is static")
-    list(APPEND NAPI_LINK_LIBS "-Wl,-whole-archive" ${HDF4_MFHDF_LIBRARY} "-Wl,-no-whole-archive")
-else()
-    list(APPEND NAPI_LINK_LIBS ${HDF4_MFHDF_LIBRARY})
-endif()
-
-list(APPEND NAPI_LINK_LIBS jpeg)
-
-include_directories ( SYSTEM ${HDF4_INCLUDE_DIRS} )
-link_directories(${HDF4_LIBRARY_DIRS})

cmake/FindMXML.cmake

@@ -1,34 +0,0 @@
-# - find MXML
-# find the MXML lib and includes
-# This module defines 
-#  LIBMXML_INCLUDE_DIR, where to find mxml.h
-#  LIBMXML_LIBRARY, library to link against
-#  LIBMXML_FOUND, if false, do not try to use the MXML lib
-
-find_path(LIBMXML_INCLUDE_DIR mxml.h
-  HINT "/usr/include"
-)
-# find position of mxml.h from the end
-string(FIND "${LIBMXML_INCLUDE_DIR}" "/mxml.h" pos REVERSE)
-# truncate the string
-string(SUBSTRING "${LIBMXML_INCLUDE_DIR}" 0 ${pos} substr)
-set(LIBMXML_INCLUDE_DIR ${substr})
-unset(substr)
-
-find_library(LIBMXML_LIBRARY mxml)
-
-# get version string
-# currently do not know from where to get it automatically
-
-# handle the QUIETLY and REQUIRED arguments and set LIBMXML_FOUND to TRUE if
-# all listed variables are TRUE
-include(${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake)
-FIND_PACKAGE_HANDLE_STANDARD_ARGS(MXML
-                                  REQUIRED_VARS LIBMXML_LIBRARY LIBMXML_INCLUDE_DIR)
-
-if (NOT LIBMXML_FOUND)
-  unset(LIBMXML_LIBRARY)
-endif()
-
-mark_as_advanced(LIBMXML_INCLUDE_DIR LIBMXML_LIBRARY)
-

cmake/FindNEXUS.cmake

@@ -1,45 +0,0 @@
-# - Find NeXus library
-# Find the native NEXUS includes and library
-# This module defines
-#  NEXUS_INCLUDE_DIR, where to find NeXus.h, etc.
-#  NEXUS_LIBRARY, library to link against to use NEXUS
-#  NEXUS_FOUND, if false, do not try to use NEXUS.
-
-find_path(NEXUS_INCLUDE_DIR napi.h
-  HINTS "/usr/local/include" "/opt/nexus/include" "/usr/local/include/nexus"
-)
-# find position of napi.h from the end
-string(FIND "${NEXUS_INCLUDE_DIR}" "/napi.h" pos REVERSE)
-# truncate the string
-string(SUBSTRING "${NEXUS_INCLUDE_DIR}" 0 ${pos} substr)
-set(NEXUS_INCLUDE_DIR ${substr})
-unset(substr)
-
-find_library(NEXUS_LIBRARY NeXus 
-  HINTS "/usr/lib" "/usr/lib64" "/usr/local/lib" "/usr/local/lib64" "/opt/nexus/lib")
-
-# get version string
-if (NEXUS_INCLUDE_DIR AND EXISTS ${NEXUS_INCLUDE_DIR}/napi.h)
-  file(STRINGS "${NEXUS_INCLUDE_DIR}/napi.h" NEXUS_version_str
-       REGEX "^#define[\t ]+NEXUS_VERSION[\t ].*")
-
-  string(REGEX REPLACE "^#define[\t ]+NEXUS_VERSION[\t ]+\"([^\"]*).*"
-         "\\1" NEXUS_VERSION_STRING "${NEXUS_version_str}")
-  unset(NEXUS_version_str)
-endif()
-
-# handle the QUIETLY and REQUIRED arguments and set NEXUS_FOUND to TRUE if
-# all listed variables are TRUE
-include(${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake)
-FIND_PACKAGE_HANDLE_STANDARD_ARGS(NEXUS
-                                  REQUIRED_VARS NEXUS_LIBRARY NEXUS_INCLUDE_DIR
-                                  VERSION_VAR NEXUS_VERSION_STRING)
-
-if (NOT NEXUS_FOUND)
-  unset(NEXUS_LIBRARY)
-endif()
-
-mark_as_advanced(NEXUS_INCLUDE_DIR NEXUS_LIBRARY)
-
-
-

doc/examples/test-asy-NeXus2.msr

@@ -1,33 +1,32 @@
-nc-ZnO T=80 F=69
+Ag_T=100_F=20
 ###############################################################
 FITPARAMETER
 #       No Name        Value     Step        Pos_Error   Boundaries
-        1 alpha       0.88008   -0.00063    0.00063     
+        1 alpha       1.02825   -0.00097    0.00098     
-        2 asym        0.1708    -0.0017     0.0017      0       0.3     
+        2 asym        0.23163   -0.00083    0.00103     0       0.3     
-        3 phase       3.90      -0.38       0.38        0       100     
+        3 phase       0.000     -0.000      0.011       0       100     
-        4 field       71.003    -0.036      0.036       0       none    
+        4 field       20.310    -0.010      0.010       0       none    
-        5 rate        0.1526    -0.0024     0.0024      0       100     
+        5 rate        0.00031   -0.00031    0.00134     0       100     
-        6 beta        1.231     -0.046      0.047       
 
 ###############################################################
 THEORY
 asymmetry      2
 TFieldCos      3  fun1       (phase frequency)
-generExpo      5     6       (rate exponent)
+simplExpo      5          (rate)
 
 ###############################################################
 FUNCTIONS
 fun1 = gamma_mu * par4
 
 ###############################################################
-RUN data/EMU00005989_v2 EMU ISIS NEXUS   (name beamline institute data-file-format)
+RUN data/emu00139040 EMU ISIS NEXUS   (name beamline institute data-file-format)
 fittype         2         (asymmetry fit)
 alpha           1
 map             0    0    0    0    0    0    0    0    0    0
-forward         1-16 
+forward         1-48 
-backward        17-32 
+backward        49-96 
 backgr.fix      0           0           
-data            40      1500    40      1500    
+data            10      2048    10      2048    
 fit             0.2     14     
 packing         1
 
@@ -39,19 +38,19 @@ SAVE
 
 ###############################################################
 FOURIER
-units            Gauss   # units either 'Gauss', 'MHz', or 'Mc/s'
+units            Gauss   # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
 fourier_power    10
 apodization      STRONG  # NONE, WEAK, MEDIUM, STRONG
-plot             REAL    # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
+plot             REAL    # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE, PHASE_OPT_REAL
 range            0    100
 phase            par2
 
 ###############################################################
 PLOT 2   (asymmetry plot)
 runs     1   
-range    0   14   -0.22   0.22
+range    0   14   -0.32   0.32
-view_packing 5
+view_packing 10
 
 ###############################################################
-STATISTIC --- 2012-03-20 10:28:41
+STATISTIC --- 2026-02-06 14:00:49
-  chisq = 796.7, NDF = 846, chisq/NDF = 0.941749
+  chisq = 1092.3, NDF = 858, chisq/NDF = 1.273055

doc/examples/test-histo-NeXus2.msr

@@ -1,23 +1,22 @@
-nc-ZnO T=80 F=69
+Ag_T=100_F=20
 ###############################################################
 FITPARAMETER
 #       No Name        Value     Step        Pos_Error   Boundaries
         1 zero        0         0           none        
-        2 phase       2.81      -0.30       0.30        0       100     
+        2 phase       0.000000011  -0.000000011 0.005772888 0       100     
-        3 field       70.998    -0.025      0.025       0       none    
+        3 field       20.3391   -0.0085     0.0085      0       none    
-        4 asym        0.1700    -0.0011     0.0012      0       0.3     
+        4 asym        0.23461   -0.00051    0.00051     0       0.3     
-        5 rate        0.1523    -0.0017     0.0017      0       100     
+        5 rate        0.0239    -0.0040     0.0035      0       100     
-        6 beta        1.255     -0.033      0.033       
+        6 Norm_L      1151.24   -0.53       0.53        
-        7 Norm_L      2410.44   -0.83       0.83        
+        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      2121.43   -0.77       0.77        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    182.29    -0.31       0.31        0       none    
 
 ###############################################################
 THEORY
 asymmetry      4
-generExpo      5     6       (rate exponent)
+simpleGss      5          (rate)
 TFieldCos   fun1  fun2       (phase frequency)
 
 ###############################################################
@@ -28,22 +27,25 @@ fun2 = gamma_mu * par3
 ###############################################################
 GLOBAL
 fittype         0         (single histogram fit)
-data            40      1500    
+data            5       2048    
-fit             0.2     14     
+t0              10.0    
+deadtime-cor    file
+fit             0.144   30     
 packing         1
 
 ###############################################################
-RUN data/EMU00005989_v2 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         1-16 
+forward         1-48 
+#deadtime-cor    file
 
-RUN data/EMU00005989_v2 XXXX ISIS NEXUS   (name beamline institute data-file-format)
+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         17-32 
+forward         49-96 
 
 ###############################################################
 COMMANDS
@@ -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   -0.22   0.22
+range    0   20   -0.35   0.35
-view_packing 2
+#view_packing 10
 
 ###############################################################
-STATISTIC --- 2019-03-12 18:08:05
+STATISTIC --- 2026-02-08 15:32:12
-  maxLH = 2585.1, NDF = 1696, maxLH/NDF = 1.524236
+  maxLH = 4233.1, NDF = 3725, maxLH/NDF = 1.136412

doc/musrfit_dox.cfg

@@ -38,7 +38,7 @@ PROJECT_NAME           = musrfit
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 1.9.10
+PROJECT_NUMBER         = 1.9.11
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -923,6 +923,18 @@ INPUT                  = musrfit.dox \
                          ../src/classes/PUserFcn.cpp \
                          ../src/external/MusrRoot/TMusrRunHeader.h \
                          ../src/external/MusrRoot/TMusrRunHeader.cpp \
+                         ../src/external/nexus/PNeXus.h \
+                         ../src/external/nexus/PNeXus.cpp \
+                         ../src/external/MuSR_software/Class_MuSR_PSI/MuSR_td_PSI_bin.h \
+                         ../src/external/MuSR_software/Class_MuSR_PSI/MuSR_td_PSI_bin.cpp \
+                         ../src/external/mud/src/mud.h \
+                         ../src/external/mud/src/mud_all.c \
+                         ../src/external/mud/src/mud.c \
+                         ../src/external/mud/src/mud_encode.c \
+                         ../src/external/mud/src/mud_friendly.c \
+                         ../src/external/mud/src/mud_gen.c \
+                         ../src/external/mud/src/mud_new.c \
+                         ../src/external/mud/src/mud_tri_ti.c \
                          ../src/addRun.cpp \
                          ../src/any2many.cpp \
                          ../src/dump_header.cpp \
@@ -2241,7 +2253,7 @@ INCLUDE_FILE_PATTERNS  =
 # recursively expanded use the := operator instead of the = operator.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-PREDEFINED             =
+PREDEFINED             = HAVE_HDF4
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The

src/classes/CMakeLists.txt

@@ -138,6 +138,7 @@ target_include_directories(
     $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/src/external/MuSR_software/Class_MuSR_PSI>
     $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/src/external/mud/src>
     $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/src/external/nexus>
+    $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}>
 )
 
 add_library(PUserFcnBase SHARED
@@ -151,6 +152,7 @@ add_library(PRgeHandler SHARED
 )
 
 #--- set target properties, e.g. version --------------------------------------
+target_compile_options(PMusr BEFORE PRIVATE "-DHAVE_CONFIG_H")
 set_target_properties(PMusr
   PROPERTIES
     VERSION ${MUSR_VERSION}

src/classes/PMsrHandler.cpp

@@ -814,6 +814,10 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
           fout.width(16);
           fout << std::left << "packing";
           fout << fGlobal.GetPacking() << std::endl;
+        } else if (sstr.BeginsWith("deadtime-cor")) {
+          fout.width(16);
+          fout << std::left << "deadtime-cor";
+          fout << fGlobal.GetDeadTimeCorrection() << std::endl;
         } else {
           fout << str.Data() << std::endl;
         }
@@ -1157,6 +1161,10 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
           fout.width(16);
           fout << std::left << "packing";
           fout << fRuns[runNo].GetPacking() << std::endl;
+        } else if (sstr.BeginsWith("deadtime-cor")) {
+          fout.width(16);
+          fout << std::left << "deadtime-cor";
+          fout << fRuns[runNo].GetDeadTimeCorrection() << std::endl;
         } else {
           fout << str.Data() << std::endl;
         }
@@ -3334,6 +3342,20 @@ Bool_t PMsrHandler::HandleGlobalEntry(PMsrLines &lines)
           error = true;
         }
       }
+    } else if (iter->fLine.BeginsWith("deadtime-cor", TString::kIgnoreCase)) { // deadtime correction
+      if (tokens->GetEntries() < 2) {
+        error = true;
+      } else {
+        ostr = dynamic_cast<TObjString*>(tokens->At(1));
+        str = ostr->GetString();
+        if (!str.CompareTo("no", TString::kIgnoreCase) ||
+            !str.CompareTo("file", TString::kIgnoreCase) ||
+            !str.CompareTo("estimate", TString::kIgnoreCase)) {
+            global.SetDeadTimeCorrection(str);
+        } else {
+          error = true;
+        }
+      }
     }
 
     // clean up
@@ -3931,6 +3953,27 @@ Bool_t PMsrHandler::HandleRunEntry(PMsrLines &lines)
       }
     }
 
+    // deadtime-correction -----------------------------------
+    if (iter->fLine.BeginsWith("deadtime-cor", TString::kIgnoreCase)) { // deadtime correction
+
+      runLinePresent = false; // this is needed to make sure that a run line is present before and ADDRUN is following
+
+      if (tokens->GetEntries() < 2) {
+        error = true;
+      } else {
+        ostr = dynamic_cast<TObjString*>(tokens->At(1));
+        str = ostr->GetString();
+        if (!str.CompareTo("no", TString::kIgnoreCase) ||
+            !str.CompareTo("file", TString::kIgnoreCase) ||
+            !str.CompareTo("estimate", TString::kIgnoreCase)) {
+            param.SetDeadTimeCorrection(str);
+        } else {
+          error = true;
+        }
+      }
+    }
+
+
     // xy-data -----------------------------------------------
     if (line.BeginsWith("xy-data", TString::kIgnoreCase)) {
 

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/dump_header.cpp

@@ -37,6 +37,7 @@
 #include <cstring>
 #include <ctime>
 #include <cassert>
+#include <cstddef>
 
 #include <iostream>
 #include <fstream>
@@ -365,15 +366,39 @@ int dump_header_root(const std::string fileName, const bool summary, const bool
 int dump_header_nexus(const std::string fileName, const bool counts) {
 
 #ifdef PNEXUS_ENABLED
-  std::unique_ptr<PNeXus> nxs_file = std::make_unique<PNeXus>(fileName.c_str());
+  nxs::HDFType type = nxs::checkHDFType(fileName);
 
-  if (nxs_file->IsValid(false)) {
+  // check for type errors, missing enabled HDF4
-    nxs_file->Dump(counts);
+  switch (type) {
-  } else {
+    case nxs::HDFType::HDF4:
-    std::cerr << std::endl;
+      std::cout << std::endl << ">> PRunDataHandler::ReadNexusFile(): HDF4 file." << std::endl;
-    std::cerr << "**ERROR** found invalid NeXus file." << std::endl;
+#ifndef HAVE_HDF4
-    std::cerr << std::endl;
+      std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): **ERROR**, HDF4 is not enabled." << std::endl;
       return 1;
+#endif
+      break;
+    case nxs::HDFType::HDF5:
+      std::cout << std::endl << ">> PRunDataHandler::ReadNexusFile(): HDF5 file." << std::endl;
+      break;
+    case nxs::HDFType::Unknown:
+      std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): Not a valid NeXus file." << std::endl;
+      return 1;
+  }
+
+  if (type == nxs::HDFType::HDF4) {
+#ifdef HAVE_HDF4
+    std::unique_ptr<nxH4::PNeXus> nxs_file = std::make_unique<nxH4::PNeXus>(fileName);
+    if (nxs_file == nullptr) {
+      std::cerr << std::endl << "**ERROR** allocation of nxH4::PNeXus object failed." << std::endl;
+    }
+    nxs_file->Dump();
+#endif
+  } else { // HDF5
+    std::unique_ptr<nxH5::PNeXus> nxs_file = std::make_unique<nxH5::PNeXus>(fileName);
+    if (nxs_file == nullptr) {
+      std::cerr << std::endl << "**ERROR** allocation of nxH5::PNeXus object failed." << std::endl;
+    }
+    nxs_file->Dump();
   }
 #else
   std::cout << std::endl << "NeXus not enabled, hence the header information cannot be dumped." << std::endl << std::endl;

src/external/nexus/CMakeLists.txt

@@ -7,7 +7,7 @@ set(prefix "${CMAKE_INSTALL_PREFIX}")
 set(exec_prefix "\$\{prefix\}")
 set(libdir "\$\{exec_prefix\}/lib")
 set(includedir "\$\{prefix\}/include")   
-set(PNEXUS_VERSION "0.9.0")
+set(PNEXUS_VERSION "1.0.0")
 set(PNEXUS_LIBRARY_NAME "PNeXus")
 configure_file("PNeXus.pc.in" "PNeXus.pc" @ONLY)
 
@@ -28,7 +28,13 @@ target_include_directories(
 )
 
 #--- add library dependencies -------------------------------------------------
-target_link_libraries(PNeXus ${NEXUS_LIBRARY})
+if (HAVE_HDF4)
+  set(HDF_LIBS ${HDF4_LIBRARIES} ${HDF5_LIBRARIES})
+else (HAVE_HDF4)   
+  set(HDF_LIBS ${HDF5_LIBRARIES})
+endif (HAVE_HDF4)
+message(STATUS "++>> HDF_LIBS: ${HDF_LIBS}")
+target_link_libraries(PNeXus ${HDF_LIBS} ${ROOT_LIBRARIES})
 
 #--- install PNeXus solib -----------------------------------------------------
 install(TARGETS PNeXus DESTINATION lib)

src/external/nexus/README.Cygwin

@@ -1,69 +0,0 @@
-2011/04/13 -- BMW
-
-Under Cygwin of all the required libraries for NeXus only HDF5 is available.
-The packages <hdf5> and <libhdf5-devel> can be installed through the Cygwin setup.
-One should also make sure that <bison>, <flex> and a package containing "/usr/lib/librpc.a" (e.g. <sunrpc> = 4.0-3) are installed.
-
-All other libraries have to be built from the sources:
-
-* JPEG-6b
-  URL: http://www.hdfgroup.org/ftp/lib-external/jpeg/src/jpegsrc.v6b.tar.gz
-  Configure options: --prefix=/usr/local --enable-static
-
-* MXML 2.5
-  URL: http://ftp.easysw.com/pub/mxml/2.5/mxml-2.5.tar.gz
-  Configure options: --prefix=/usr/local --enable-static
-
-* HDF 4.2.5
-  URL: http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/hdf-4.2.5.tar.gz 
-  Configure options: --prefix=/usr/local --enable-static --disable-fortran --with-jpeg=/usr/local
-
-* NeXus 4.2.1
-  URL: http://download.nexusformat.org/kits/nexus-4.2.1.tar.gz
-  Configure options: --prefix=/usr/local --with-hdf4=/usr/local --with-hdf5=/usr --with-xml=/usr/local
-
-The version numbers and source-code locations might of course change with time but should be easily adjustable.
-
-If one is confident enough that all requirements to build the above packages are fullfilled, one could also try to run the following lines as a script.
-However, there is absolutely no warranty that it works.
-
----
-
-#!/bin/sh
-
-cd
-mkdir nexus
-cd nexus
-curl http://www.hdfgroup.org/ftp/lib-external/jpeg/src/jpegsrc.v6b.tar.gz -G | tar xz
-cd jpeg-6b
-./configure --prefix=/usr/local --enable-static
-make
-make install
-cd ..
-curl http://ftp.easysw.com/pub/mxml/2.5/mxml-2.5.tar.gz -G | tar xz
-cd mxml-2.5
-./configure --prefix=/usr/local --enable-static
-make
-make install
-cd ..
-curl http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/hdf-4.2.5.tar.gz -G | tar xz
-cd hdf-4.2.5
-./configure --prefix=/usr/local --enable-static --disable-fortran --with-jpeg=/usr/local
-make
-make install
-cd ..
-curl http://download.nexusformat.org/kits/nexus-4.2.1.tar.gz -G | tar xz
-./configure --prefix=/usr/local --with-hdf4=/usr/local --with-hdf5=/usr --with-xml=/usr/local
-make
-make install
-
----
-
-In order to obtain NeXus support in musrfit after installing the above libraries, musrfit has to be configured with the options
-"--enable-static --enable-NeXus"
-
-Further information on how to set up musrfit under Cygwin can be found here:
-https://intranet.psi.ch/MUSR/MusrFitSetup#A_4_MS_Windows
-http://lmu.web.psi.ch/facilities/software/musrfit/user/intranet.psi.ch/MUSR/MusrFitSetup.html#A_4_MS_Windows
-
-EOF

src/external/nexus/examples/hdf4/CMakeLists.txt

@@ -0,0 +1,149 @@
+# - h4nexus
+cmake_minimum_required(VERSION 3.26)
+
+project(h4nexus VERSION 0.1.0 LANGUAGES CXX)
+
+#--- set C++ standard ---------------------------------------------------------
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+#--- set a default build type if none was specified ---------------------------
+set(default_build_type "Release")
+
+if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  message(STATUS "Setting build type to '${default_build_type}' as none was specified.")
+  set(CMAKE_BUILD_TYPE "${default_build_type}" CACHE
+      STRING "Choose the type of build." FORCE)
+  # Set the possible values of build type for cmake-gui
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
+    "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+endif ()
+
+#--- check for pkg-config -----------------------------------------------------
+find_package(PkgConfig REQUIRED)
+
+#--- check for git ------------------------------------------------------------
+find_package(Git REQUIRED)
+
+#--- check for HDF4 -----------------------------------------------------------
+# Find HDF4 manually (pkg-config often doesn't have hdf4)
+find_path(HDF4_INCLUDE_DIR
+  NAMES mfhdf.h
+  PATHS /usr/include /usr/local/include
+  PATH_SUFFIXES hdf
+)
+
+find_library(HDF4_DF_LIBRARY
+  NAMES df libdf
+  PATHS /usr/lib64 /usr/lib /usr/local/lib64 /usr/local/lib
+)
+
+find_library(HDF4_MFHDF_LIBRARY
+  NAMES mfhdf libmfhdf
+  PATHS /usr/lib64 /usr/lib /usr/local/lib64 /usr/local/lib
+)
+
+if (HDF4_INCLUDE_DIR AND HDF4_DF_LIBRARY AND HDF4_MFHDF_LIBRARY)
+    set(HDF4_FOUND TRUE)
+    set(HDF4_INCLUDE_DIRS ${HDF4_INCLUDE_DIR})
+    set(HDF4_LIBRARIES ${HDF4_MFHDF_LIBRARY} ${HDF4_DF_LIBRARY})
+    message(STATUS "Found HDF4: ${HDF4_INCLUDE_DIR}")
+    message(STATUS "  HDF4 libraries: ${HDF4_LIBRARIES}")
+else ()
+    message(FATAL_ERROR "HDF4 library not found. Please install libhdf4-dev or hdf-devel")
+endif ()
+
+include_directories(${HDF4_INCLUDE_DIRS})
+
+#--- check for HDF5 -----------------------------------------------------------
+find_package(HDF5 REQUIRED COMPONENTS CXX)
+if(NOT HDF5_FOUND)
+    message(FATAL_ERROR "HDF5 C++ library not found")
+endif()
+include_directories(${HDF5_INCLUDE_DIRS})
+
+#--- check for ROOT -----------------------------------------------------------
+find_package(ROOT 6.36 REQUIRED COMPONENTS Minuit2)
+if (ROOT_miniut2_FOUND)
+  execute_process(COMMAND root-config --bindir OUTPUT_VARIABLE ROOT_BINDIR)
+  string(STRIP ${ROOT_BINDIR} ROOT_BINDIR)
+  execute_process(COMMAND root-config --version OUTPUT_VARIABLE ROOT_VERSION)
+  string(STRIP ${ROOT_VERSION} ROOT_VERSION)
+  message("-- Found ROOT: ${ROOT_BINDIR} (found version: ${ROOT_VERSION})")
+  #---Define useful ROOT functions and macros (e.g. ROOT_GENERATE_DICTIONARY)
+  include(${ROOT_USE_FILE})
+endif (ROOT_miniut2_FOUND)
+
+#--- all checks done -> feed config.h -----------------------------------------
+set(HAVE_CONFIG_H 1 CACHE INTERNAL "config.h is available")
+configure_file(${CMAKE_SOURCE_DIR}/cmake/config.h.in ${CMAKE_CURRENT_BINARY_DIR}/config.h)
+
+#--- check if project source is a git repo ------------------------------------
+if (EXISTS "${CMAKE_SOURCE_DIR}/.git/HEAD")
+  message(STATUS "is a git repo")
+  set(IS_GIT_REPO 1)
+else ()
+  message(STATUS "is NOT a git repo")
+  set(IS_GIT_REPO 0)
+endif ()
+
+#--- start create git-revision.h ----------------------------------------------
+if (IS_GIT_REPO)
+  execute_process(COMMAND sh ${CMAKE_SOURCE_DIR}/git_revision.sh ${CMAKE_BINARY_DIR})
+
+  set(HAVE_GIT_REV_H "-DHAVE_GIT_REV_H")
+  set(GIT_REV_H "git-revision.h")
+else (IS_GIT_REPO)
+  set(HAVE_GIT_REV_H "")
+  set(GIT_REV_H "")
+endif (IS_GIT_REPO)
+
+#--- end create git-revision.h ------------------------------------------------
+
+#--- write summary of the installation
+cmake_host_system_information(RESULT PROCESSOR QUERY PROCESSOR_DESCRIPTION)
+
+message("")
+message("|-----------------------------------------------------------------------|")
+message("|                                                                       |")
+message("|                            Summary                                    |")
+message("|                                                                       |")
+message("|-----------------------------------------------------------------------|")
+message("")
+message(" System:    ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
+message(" Processor: ${PROCESSOR} (${CMAKE_SYSTEM_PROCESSOR})")
+message(" ----------")
+message("")
+message(" h4nexus Version: ${h4nexus_VERSION}")
+message(" ----------------")
+message("")
+message(" Build Type: ${CMAKE_BUILD_TYPE}")
+message(" -----------")
+message("")
+message(" Requirements:")
+message(" -------------")
+message("")
+message(" HDF4    found in ${HDF4_INCLUDE_DIRS}")
+message(" ROOT    found in ${ROOT_INCLUDE_DIRS}, Version: ${ROOT_VERSION}")
+message("")
+message(" Installation directories:")
+message(" -------------------------")
+message("")
+message(" Programs                : ${CMAKE_INSTALL_PREFIX}/bin")
+message("")
+message("-------------------------------------------------------------------------")
+message("")
+
+#--- h4nexus executable -------------------------------------------------------
+add_executable(h4nexus 
+               ../../PNeXus.cpp
+               main.cpp)
+target_compile_options(h4nexus BEFORE PRIVATE "-DHAVE_HDF4 -DHAVE_CONFIG_H" ${HAVE_GIT_REV_H})
+target_include_directories(h4nexus 
+  BEFORE PRIVATE
+    $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/build>
+    $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/../..>
+    $<BUILD_INTERFACE:${ROOT_INCLUDE_DIRS}>
+)
+target_link_libraries(h4nexus ${HDF4_LIBRARIES} ${HDF5_LIBRARIES} ${ROOT_LIBRARIES})

src/external/nexus/examples/hdf4/cmake/config.h.in

@@ -0,0 +1,7 @@
+/* config.h.in.  Generated from CMakeLists.txt  */
+
+/* Define to 1 if you have the <config.h> file. */
+#cmakedefine HAVE_CONFIG_H @HAVE_CONFIG_H@
+
+/* h4nexus version */
+#define H4NEXUS_VERSION "@h4nexus_VERSION@"

src/external/nexus/examples/hdf4/docu/README.md

@@ -0,0 +1,155 @@
+# h4nexus - handle muSR-NeXus files via HDF4 only
+
+## Contents
+
+Tests and classes to handle muSR-NeXus files directly via the HDF4 C API.
+
+This project provides the same API as h5nexus but uses HDF4 instead of HDF5 for handling NeXus files.
+
+## Features
+
+- **Read and write NeXus HDF4 files** with a clean C++ API
+- **Case-insensitive path lookup** for datasets and groups
+- **Type-safe data handling** using template classes
+- **Dead time correction calculation** for muon detector data using ROOT Minuit2
+- **Compatible API with h5nexus** for easy migration
+
+## Key Classes
+
+- `nxH4::PNeXus` - Main class for reading/writing NeXus HDF4 files
+- `nxH4::PNXdata<T>` - Template class for storing dataset content with attributes
+- `nxH4::PNeXusDeadTime` - Dead time correction calculator for muon detector data
+
+## Requirements
+
+- CMake >= 3.26
+- C++17 compatible compiler
+- HDF4 library (libhdf4-dev or hdf-devel)
+- ROOT >= 6.36 with Minuit2 component
+- pkg-config
+
+## Building
+
+```bash
+mkdir build
+cd build
+cmake ..
+make
+```
+
+## Installation
+
+```bash
+make install
+```
+
+This will install:
+- Library: `libh4nexus.so` in `${CMAKE_INSTALL_PREFIX}/lib`
+- Executable: `h4nexus` in `${CMAKE_INSTALL_PREFIX}/bin`
+- Header: `PNeXus.h` in `${CMAKE_INSTALL_PREFIX}/include/h4nexus`
+
+## Usage
+
+### Command Line
+
+```bash
+# Display help
+h4nexus --help
+
+# Read and display a NeXus HDF4 file
+h4nexus --fn input.nxs
+
+# Read with debug output
+h4nexus --fn input.nxs --debug
+
+# Calculate dead time corrections
+h4nexus --fn input.nxs --dead_time_estimate
+
+# Write output file
+h4nexus --fn input.nxs --out output.nxs
+```
+
+### Programmatic Usage
+
+```cpp
+#include <h4nexus/PNeXus.h>
+
+// Read a NeXus file
+nxH4::PNeXus nexus("data.nxs");
+
+// Access datasets
+auto counts_data = nexus.GetDataset<int>("/raw_data_1/detector_1/counts");
+const auto& counts = counts_data.GetData();
+const auto& dims = counts_data.GetDimensions();
+
+// Dump file contents
+nexus.Dump();
+
+// Write to new file
+nexus.WriteNexusFile("output.nxs", 2);  // IDF version 2
+```
+
+### Creating Files from Scratch
+
+```cpp
+nxH4::PNeXus nxs_out;
+
+// Add datasets
+std::vector<int> counts(16*66000, 0);
+nxs_out.AddDataset<int>("/raw_data_1/detector_1/counts",
+                        counts, {1, 16, 66000},
+                        nxH4::H4DataType::INT32);
+
+// Add attributes
+nxs_out.AddDatasetAttribute<int>("/raw_data_1/detector_1/counts",
+                                  "units", std::string("counts"));
+
+// Add group attributes
+nxs_out.AddGroupAttribute("/raw_data_1", "NX_class", std::string("NXentry"));
+
+// Write file
+nxs_out.WriteNexusFile("output.nxs");
+```
+
+## API Compatibility with h5nexus
+
+The h4nexus API is designed to be compatible with h5nexus. The main differences are:
+
+- Namespace: `nxH4::` instead of `nxH5::`
+- Data types: `H4DataType` enum instead of `H5::DataType`
+- Dimensions: Uses `uint32_t` instead of `hsize_t`
+
+Code migration typically requires only:
+1. Changing namespace from `nxH5` to `nxH4`
+2. Changing `H5::PredType::NATIVE_INT` to `nxH4::H4DataType::INT32` (etc.)
+3. Changing dimension types from `hsize_t` to `uint32_t`
+
+## Supported Data Types
+
+- `H4DataType::INT32` - 32-bit signed integer
+- `H4DataType::FLOAT32` - 32-bit floating point
+- `H4DataType::FLOAT64` - 64-bit floating point
+- `H4DataType::CHAR8` - 8-bit character/string
+- `H4DataType::UINT32` - 32-bit unsigned integer
+- `H4DataType::INT16` - 16-bit signed integer
+- `H4DataType::UINT16` - 16-bit unsigned integer
+- `H4DataType::INT8` - 8-bit signed integer
+- `H4DataType::UINT8` - 8-bit unsigned integer
+
+## Differences from HDF5
+
+HDF4 has some limitations compared to HDF5:
+- No true hierarchical groups (simulated using naming conventions)
+- Less flexible attribute handling
+- Different maximum name lengths
+- C API instead of C++ API
+
+The h4nexus library abstracts these differences to provide a similar interface to h5nexus.
+
+## License
+
+GNU General Public License v2 (GPLv2)
+
+## Contacts
+
+Andreas Suter <andreas.suter@psi.ch>

src/external/nexus/examples/hdf4/git_revision.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+# Script to create git-revision.h with current git information
+# Usage: git_revision.sh [output_directory]
+
+output_dir="${1:-.}"
+output_file="${output_dir}/git-revision.h"
+
+# Check if we're in a git repository
+if ! git rev-parse --git-dir > /dev/null 2>&1; then
+    echo "Not in a git repository, skipping git-revision.h generation"
+    exit 0
+fi
+
+# Get git information
+git_branch=$(git rev-parse --abbrev-ref HEAD 2>/dev/null)
+git_hash=$(git rev-parse --short HEAD 2>/dev/null)
+git_date=$(git log -1 --format=%cd --date=short 2>/dev/null)
+
+# Create header file
+cat > "$output_file" << EOF
+// This file is auto-generated by git_revision.sh
+// Do not edit manually
+
+#ifndef GIT_REVISION_H
+#define GIT_REVISION_H
+
+#define GIT_BRANCH "$git_branch"
+#define GIT_HASH "$git_hash"
+#define GIT_DATE "$git_date"
+
+#endif // GIT_REVISION_H
+EOF
+
+echo "Generated $output_file"

src/external/nexus/examples/hdf4/main.cpp

@@ -0,0 +1,447 @@
+/***************************************************************************
+
+  main.cpp
+
+  Author: Andreas Suter
+  e-mail: andreas.suter@psi.ch
+
+***************************************************************************/
+
+/***************************************************************************
+ *   Copyright (C) 2007-2026 by Andreas Suter                              *
+ *   andreas.suter@psi.ch                                                  *
+ *                                                                         *
+ *   This program is free software; you can redistribute it and/or modify  *
+ *   it under the terms of the GNU General Public License as published by  *
+ *   the Free Software Foundation; either version 2 of the License, or     *
+ *   (at your option) any later version.                                   *
+ *                                                                         *
+ *   This program is distributed in the hope that it will be useful,       *
+ *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
+ *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
+ *   GNU General Public License for more details.                          *
+ *                                                                         *
+ *   You should have received a copy of the GNU General Public License     *
+ *   along with this program; if not, write to the                         *
+ *   Free Software Foundation, Inc.,                                       *
+ *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
+ ***************************************************************************/
+
+/**
+ * @file main.cpp
+ * @brief Command-line interface for the h4nexus NeXus HDF4 file reader/writer
+ *
+ * This file contains the main() function and command-line interface for the
+ * h4nexus program. It provides functionality to:
+ * - Read and display NeXus HDF4 files
+ * - Write NeXus HDF4 files using the PNXdata approach
+ * - Calculate dead time corrections for muon detector data
+ *
+ * **Command-Line Options:**
+ * - --fn <file>: Input NeXus HDF4 file (required)
+ * - --out <file>: Output NeXus HDF4 file (optional)
+ * - --debug, -d: Enable debug output
+ * - --dead_time_estimate, -dt: Calculate dead time corrections
+ * - --help, -h: Display help message
+ * - --version, -v: Display version information
+ *
+ * @author Andreas Suter
+ * @date 2007-2026
+ * @copyright GNU General Public License v2
+ * @version 1.0
+ *
+ * @see nxH4::PNeXus
+ * @see nxH4::PNeXusDeadTime
+ */
+
+#include <cstring>
+#include <iostream>
+#include <string>
+#include <memory>
+#include <ctime>
+
+#include <mfhdf.h>
+
+#include "PNeXus.h"
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#ifdef HAVE_GIT_REV_H
+#include "git-revision.h"
+#endif
+
+//-----------------------------------------------------------------------------
+/**
+ * @brief Display command-line syntax and help information
+ *
+ * Prints the usage syntax and available command-line options for the h4nexus
+ * program to stdout and exits the program.
+ */
+void h4nexus_syntax() {
+  std::cout << std::endl;
+  std::cout << "usage: h4nexus [--help | -h] |" << std::endl;
+  std::cout << "               [--version | -v] |" << std::endl;
+  std::cout << "               --fn <fln> [--debug | -d]" << std::endl;
+  std::cout << "               [--dead_time_estimate | -dt]]" << std::endl;
+  std::cout << "               [--out <fout>]" << std::endl;
+  std::cout << std::endl;
+  std::cout << "options:" << std::endl;
+  std::cout << "  --help, -h: this help." << std::endl;
+  std::cout << "  --version, -v: version of h4nexus." << std::endl;
+  std::cout << "  --fn <fln>: nexus hdf4 input file name <fn>." << std::endl;
+  std::cout << "  --dead_time_estimate, -dt: dead time estimate for the read hdf4 nexus file." << std::endl;
+  std::cout << "  --debug, -d: print additional debug information." << std::endl;
+  std::cout << "  --out <fout>: write the required datasets of a nexus hdf4 file to file " << std::endl;
+  std::cout << "                with name <fout>. Only makes sense together with the option --fn <fln>." << std::endl;
+  std::cout << std::endl;
+  exit(0);
+}
+
+//-----------------------------------------------------------------------------
+/**
+ * @brief Calculate dead time corrections for muon detector data
+ *
+ * Estimates dead time corrections for each detector in the NeXus file using
+ * the PNeXusDeadTime class and ROOT Minuit2 minimization.
+ *
+ * @param nxs Pointer to the PNeXus object containing the data
+ * @param debug If true, print additional debug information
+ *
+ * @see nxH4::PNeXusDeadTime
+ */
+void h4nexus_deadTimeEstimate(const nxH4::PNeXus *nxs, bool debug)
+{
+  if (debug) {
+    std::cout << std::endl;
+    std::cout << std::endl << "+++++++++++++++++++";
+    std::cout << std::endl << "in deadTimeEstimate";
+    std::cout << std::endl << "+++++++++++++++++++";
+    std::cout << std::endl;
+  }
+
+  nxH4::PNeXusDeadTime ndt(nxs, debug);
+  auto dims = ndt.GetDimensions();
+  for (unsigned int i=0; i<dims[1]; i++) {
+    ndt.minimize(i);
+  }
+}
+
+//-----------------------------------------------------------------------------
+/**
+ * @brief Write NeXus HDF4 file using the PNXdata approach
+ *
+ * Writes all datasets from the PNeXus data map to a new NeXus HDF4 file.
+ * This function uses the WriteNexusFile() method to create a complete
+ * NeXus file with all groups, datasets, and attributes.
+ *
+ * @param nxs Pointer to the PNeXus object containing the data to write
+ * @param outFileName Output filename for the NeXus HDF4 file
+ * @param debug If true, print additional debug information
+ *
+ * @note Currently only supports IDF version 2 files
+ *
+ * @see nxH4::PNeXus::WriteNexusFile()
+ */
+void h4nexus_writeTest(const nxH4::PNeXus *nxs, const std::string& outFileName, bool debug)
+{
+  if (debug) {
+    std::cout << std::endl;
+    std::cout << "++++++++++++++++++++" << std::endl;
+    std::cout << "Writing NeXus file" << std::endl;
+    std::cout << "++++++++++++++++++++" << std::endl;
+    std::cout << std::endl;
+  }
+
+  if (nxs->GetIdfVersion() == 1) {
+    std::cerr << "Error: IDF v1 write not yet implemented" << std::endl;
+    return;
+  }
+
+  // Write using the read object's data
+  int result = const_cast<nxH4::PNeXus*>(nxs)->WriteNexusFile(outFileName, nxs->GetIdfVersion());
+
+  if (result == 0) {
+    std::cout << "Successfully wrote: " << outFileName << std::endl;
+  } else {
+    std::cerr << "Failed to write file: " << outFileName << std::endl;
+  }
+
+  // write data from scratch
+
+  std::unique_ptr<nxH4::PNeXus> nxs_out = std::make_unique<nxH4::PNeXus>();
+
+  std::vector<int> ival;
+  std::vector<float> fval;
+  std::vector<std::string> sval;
+
+  // ----------
+  // raw_data_1
+  // ----------
+
+  // IDF version
+  ival.push_back(2);
+  nxs_out->AddDataset<int>("/raw_data_1/IDF_version", ival, {1}, nxH4::H4DataType::INT32);
+  ival.clear();
+
+  // add group attribute to '/raw_data_1'
+  nxs_out->AddGroupAttribute("/raw_data_1", "NX_class", std::string("NXentry"));
+
+  // beamline
+  sval.push_back("piE3");
+  nxs_out->AddDataset<std::string>("/raw_data_1/beamline", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // definition
+  sval.push_back("muonTD");
+  nxs_out->AddDataset<std::string>("/raw_data_1/definition", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // run_number
+  ival.push_back(1234);
+  nxs_out->AddDataset<int>("/raw_data_1/run_number", ival, {1}, nxH4::H4DataType::INT32);
+  ival.clear();
+
+  // title
+  sval.push_back("this is the run title.");
+  nxs_out->AddDataset<std::string>("/raw_data_1/title", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // start time
+  sval.push_back("2026-01-01T01:02:03");
+  nxs_out->AddDataset<std::string>("/raw_data_1/start_time", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // end time
+  sval.push_back("2026-01-01T02:03:42");
+  nxs_out->AddDataset<std::string>("/raw_data_1/end_time", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // experiment_identifier - pgroup for PSI
+  sval.push_back("p18324");
+  nxs_out->AddDataset<std::string>("/raw_data_1/experiment_identifier", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // -------------------
+  // detector_1 (NXdata)
+  // -------------------
+
+  // add group attribute to /raw_data_1/instrument
+  nxs_out->AddGroupAttribute("/raw_data_1/detector_1", "NX_class", std::string("NXdata"));
+
+  // counts
+  std::vector<int> counts(16*66000, 42); // data 16 histos with length 66000
+  nxs_out->AddDataset<int>("/raw_data_1/detector_1/counts", counts, {1, 16, 66000}, nxH4::H4DataType::INT32);
+
+  // attributes for counts
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "signal", 1);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "axes", std::string("period_index,spectrum_index,raw_time"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "long_name", std::string("positron_counts"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "t0_bin", 2741);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "first_good_bin", 2741);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "last_good_bin", 66000);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "units", std::string("counts"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "target", std::string("/raw_data_1/instrument/detector_1/counts"));
+
+  // raw_time
+  std::vector<float> raw_time(66000, 0.0);
+  for (unsigned int i=0; i<raw_time.size(); i++)
+    raw_time[i] = 0.1953125f*1.0e-3*((float)i-2741.0f+0.5f);
+  nxs_out->AddDataset<float>("/raw_data_1/detector_1/raw_time", raw_time, {66000}, nxH4::H4DataType::FLOAT32);
+
+  // attributes raw_time
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/detector_1/raw_time", "units", std::string("microseconds"));
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/detector_1/raw_time", "target", std::string("/raw_data_1/instrument/detector_1/raw_time"));
+
+
+  // ----------
+  // instrument
+  // ----------
+
+  // add group attribute to /raw_data_1/instrument
+  nxs_out->AddGroupAttribute("/raw_data_1/instrument", "NX_class", std::string("NXinstrument"));
+
+  // name
+  sval.push_back("LEM");
+  nxs_out->AddDataset<std::string>("/raw_data_1/instrument/name", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // ------
+  // source
+  // ------
+
+  // add group attribute to /raw_data_1/instrument/source
+  nxs_out->AddGroupAttribute("/raw_data_1/instrument/source", "NX_class", std::string("NXsource"));
+
+  // name
+  sval.push_back("PSI");
+  nxs_out->AddDataset<std::string>("/raw_data_1/instrument/source/name", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // type
+  sval.push_back("continuous muon source");
+  nxs_out->AddDataset<std::string>("/raw_data_1/instrument/source/types", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // probe
+  sval.push_back("postive muons");
+  nxs_out->AddDataset<std::string>("/raw_data_1/instrument/source/probe", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // -----------------------
+  // detector_1 (NXdetector)
+  // -----------------------
+
+  // add group attribute to /raw_data_1/instrument/detector_1
+  nxs_out->AddGroupAttribute("/raw_data_1/instrument/detector_1", "NX_class", std::string("NXdetector"));
+
+  // counts
+  nxs_out->AddDataset<int>("/raw_data_1/instrument/detector_1/counts", counts, {1, 16, 66000}, nxH4::H4DataType::INT32);
+
+  // attributes for counts
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "signal", 1);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "axes", std::string("period_index,spectrum_index,raw_time"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "long_name", std::string("positron_counts"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "t0_bin", 2741);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "first_good_bin", 2741);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "last_good_bin", 66000);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "units", std::string("counts"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "target", std::string("/raw_data_1/instrument/detector_1/counts"));
+
+  // raw_time
+  nxs_out->AddDataset<float>("/raw_data_1/instrument/detector_1/raw_time", raw_time, {66000}, nxH4::H4DataType::FLOAT32);
+
+  // attributes raw_time
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/raw_time", "units", std::string("microseconds"));
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/raw_time", "target", std::string("/raw_data_1/instrument/detector_1/raw_time"));
+
+  // resolution
+  fval.push_back(195.3125);
+  nxs_out->AddDataset<float>("/raw_data_1/instrument/detector_1/resolution", fval, {1}, nxH4::H4DataType::FLOAT32);
+  fval.clear();
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/resolution",
+                                      "units", std::string("picoseconds"));
+
+  // spectrum_index
+  for (unsigned int i=0; i<16; i++)
+    ival.push_back(i+1);
+  nxs_out->AddDataset<int>("/raw_data_1/instrument/detector_1/spectrum_index", ival, {16}, nxH4::H4DataType::INT32);
+  ival.clear();
+
+  // dead_time
+  std::vector<float> deadTime(16, 0.0);
+  nxs_out->AddDataset<float>("/raw_data_1/instrument/detector_1/dead_time", deadTime, {16}, nxH4::H4DataType::FLOAT32);
+
+  // attributes dead_time
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/dead_time", "available", 0);
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/dead_time", "units", std::string("microseconds"));
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/dead_time", "target", std::string("/raw_data_1/instrument/detector_1/dead_time"));
+
+  // add root attributes
+  // file name
+  nxs_out->AddRootAttribute("file_name", std::string("_test.nxs"));
+  // date-time
+  std::time_t time = std::time({});
+  char timeString[std::size("yyyy-mm-ddThh:mm:ssZ")];
+  std::strftime(std::data(timeString), std::size(timeString),
+                 "%FT%TZ", std::gmtime(&time));
+  nxs_out->AddRootAttribute("file_time", std::string(timeString));
+  // NeXus version
+  nxs_out->AddRootAttribute("NeXus_Version", std::string("4.3.0"));
+  // hdf4 version
+  nxs_out->AddRootAttribute("HDF4_Version", std::string(nxs->GetHdf4Version()));
+  // creator
+  nxs_out->AddRootAttribute("creator", std::string("h4nexus - PSI"));
+
+  nxs_out->WriteNexusFile("_test.nxs");
+}
+
+//-----------------------------------------------------------------------------
+/**
+ * @brief Main entry point for the h4nexus program
+ *
+ * Parses command-line arguments and performs the requested operations:
+ * - Read and display NeXus HDF4 file information
+ * - Write NeXus HDF4 files with modified data
+ * - Calculate dead time corrections
+ *
+ * @param argc Number of command-line arguments
+ * @param argv Array of command-line argument strings
+ *
+ * @return 0 on success, non-zero on error
+ *
+ * @see h4nexus_syntax() for available command-line options
+ */
+int main(int argc, char *argv[])
+{
+  std::string fileName{""};
+  std::string fileNameOut{""};
+  bool printDebug{false};
+  bool deadTimeEstimate{false};
+
+  if (argc == 1)
+    h4nexus_syntax();
+
+  for (int i=1; i<argc; i++) {
+    if (!strcmp(argv[i], "-h") || !strcmp(argv[i], "--help")) {
+      h4nexus_syntax();
+    } else if (!strcmp(argv[i], "-v") || !strcmp(argv[i], "--version")) {
+#ifdef HAVE_CONFIG_H
+#ifdef HAVE_GIT_REV_H
+      std::cout << std::endl << "h4nexus version: " << H4NEXUS_VERSION << ", git-branch: " << GIT_BRANCH << ", git-hash: " << GIT_HASH << std::endl << std::endl;
+#else
+      std::cout << std::endl << "h4nexus version: " << H4NEXUS_VERSION << std::endl << std::endl;
+#endif
+#else
+#ifdef HAVE_GIT_REV_H
+      std::cout << std::endl << "h4nexus git-branch: " << GIT_BRANCH << ", git-hash: " << GIT_HASH << std::endl << std::endl;
+#else
+      std::cout << std::endl << "h4nexus version: unknown." << std::endl << std::endl;
+#endif
+#endif
+      return 0;
+    } else if (!strcmp(argv[i], "--fn")) {
+      if (i+1 >= argc) {
+        std::cout << std::endl << "**ERROR** found --fn without <fln>." << std::endl;
+        h4nexus_syntax();
+      }
+      i++;
+      fileName = argv[i];
+    } else if (!strcmp(argv[i], "-dt") || !strcmp(argv[i], "--dead_time_estimate")) {
+      deadTimeEstimate = true;
+    } else if (!strcmp(argv[i], "-d") || !strcmp(argv[i], "--debug")) {
+        printDebug = true;
+    } else if (!strcmp(argv[i], "--out")) {
+      if (i+1 >= argc) {
+        std::cout << std::endl << "**ERROR** found --out without <fout>." << std::endl;
+        h4nexus_syntax();
+      }
+      i++;
+      fileNameOut = argv[i];
+    } else {
+      h4nexus_syntax();
+    }
+  }
+
+  if (fileName.empty()) {
+    std::cerr << std::endl;
+    std::cerr << "**ERROR** <fln> is missing." << std::endl;
+    std::cerr << std::endl;
+    h4nexus_syntax();
+  }
+
+  std::unique_ptr<nxH4::PNeXus> nxs = std::make_unique<nxH4::PNeXus>(fileName, printDebug);
+
+  nxs->Dump();
+
+  if (deadTimeEstimate) {
+    h4nexus_deadTimeEstimate(nxs.get(), printDebug);
+  }
+
+  if (!fileNameOut.empty()) {
+    h4nexus_writeTest(nxs.get(), fileNameOut, printDebug);
+  }
+
+  return 0;
+}

src/external/nexus/examples/hdf5/CMakeLists.txt

@@ -0,0 +1,119 @@
+# - h5nexus
+cmake_minimum_required(VERSION 3.26)
+
+project(h5nexus VERSION 0.1.0 LANGUAGES CXX)
+
+#--- set C++ standard ---------------------------------------------------------
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+#--- set a default build type if none was specified ---------------------------
+set(default_build_type "Release")
+
+if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  message(STATUS "Setting build type to '${default_build_type}' as none was specified.")
+  set(CMAKE_BUILD_TYPE "${default_build_type}" CACHE
+      STRING "Choose the type of build." FORCE)
+  # Set the possible values of build type for cmake-gui
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
+    "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+endif ()
+
+#--- check for pkg-config -----------------------------------------------------
+find_package(PkgConfig REQUIRED)
+
+#--- check for git ------------------------------------------------------------
+find_package(Git REQUIRED)
+
+#--- check for HDF5 -----------------------------------------------------------
+find_package(HDF5 REQUIRED COMPONENTS CXX)
+if(NOT HDF5_FOUND)
+    message(FATAL_ERROR "HDF5 C++ library not found")
+endif()
+include_directories(${HDF5_INCLUDE_DIRS})
+
+#--- check for ROOT -----------------------------------------------------------
+find_package(ROOT 6.36 REQUIRED COMPONENTS Minuit2)
+if (ROOT_miniut2_FOUND)
+  execute_process(COMMAND root-config --bindir OUTPUT_VARIABLE ROOT_BINDIR)
+  string(STRIP ${ROOT_BINDIR} ROOT_BINDIR)
+  execute_process(COMMAND root-config --version OUTPUT_VARIABLE ROOT_VERSION)
+  string(STRIP ${ROOT_VERSION} ROOT_VERSION)
+  message("-- Found ROOT: ${ROOT_BINDIR} (found version: ${ROOT_VERSION})")
+  #---Define useful ROOT functions and macros (e.g. ROOT_GENERATE_DICTIONARY)
+  include(${ROOT_USE_FILE})
+endif (ROOT_miniut2_FOUND)
+
+#--- all checks done -> feed config.h -----------------------------------------
+set(HAVE_CONFIG_H 1 CACHE INTERNAL "config.h is available")
+configure_file(${CMAKE_SOURCE_DIR}/cmake/config.h.in ${CMAKE_CURRENT_BINARY_DIR}/config.h)
+
+#--- check if project source is a git repo ------------------------------------
+if (EXISTS "${CMAKE_SOURCE_DIR}/.git/HEAD")
+  message(STATUS "is a git repo")
+  set(IS_GIT_REPO 1)
+else ()
+  message(STATUS "is NOT a git repo")
+  set(IS_GIT_REPO 0)
+endif ()
+
+#--- start create git-revision.h ----------------------------------------------
+if (IS_GIT_REPO)
+  execute_process(COMMAND sh ${CMAKE_SOURCE_DIR}/src/git_revision.sh)
+
+  set(HAVE_GIT_REV_H "-DHAVE_GIT_REV_H")  
+  set(GIT_REV_H "git-revision.h")
+else (IS_GIT_REPO)
+  set(HAVE_GIT_REV_H "")  
+  set(GIT_REV_H "")
+endif (IS_GIT_REPO)
+
+#--- end create git-revision.h ------------------------------------------------
+
+#--- write summary of the installation
+cmake_host_system_information(RESULT PROCESSOR QUERY PROCESSOR_DESCRIPTION)
+
+message("")
+message("|-----------------------------------------------------------------------|")
+message("|                                                                       |")
+message("|                            Summary                                    |")
+message("|                                                                       |")
+message("|-----------------------------------------------------------------------|")
+message("")
+message(" System:    ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
+message(" Processor: ${PROCESSOR} (${CMAKE_SYSTEM_PROCESSOR})")
+message(" ----------")
+message("")
+message(" h5nexus Version: ${musrfit_VERSION}")
+message(" ----------------")
+message("")
+message(" Build Type: ${CMAKE_BUILD_TYPE}")
+message(" -----------")
+message("")
+message(" Requirements:")
+message(" -------------")
+message("")
+message(" HDF5    found in ${HDF5_INCLUDE_DIRS}, Version: ${HDF5_VERSION}")
+message(" ROOT    found in ${ROOT_INCLUDE_DIRS}, Version: ${ROOT_VERSION}")
+message("")
+message(" Installation directories:")
+message(" -------------------------")
+message("")
+message(" Programs                : ${CMAKE_INSTALL_PREFIX}/bin")
+message("")
+message("-------------------------------------------------------------------------")
+message("")
+
+#--- add executable -----------------------------------------------------------
+add_executable(h5nexus 
+               ../../PNeXus.cpp
+               main.cpp)
+target_compile_options(h5nexus BEFORE PRIVATE "-DHAVE_CONFIG_H" "${HAVE_GIT_REV_H}")
+target_include_directories(h5nexus 
+  BEFORE PRIVATE
+    $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/build>
+    $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/../..>
+    $<BUILD_INTERFACE:${ROOT_INCLUDE_DIRS}>
+)
+target_link_libraries(h5nexus ${HDF5_CXX_LIBRARIES} ${ROOT_LIBRARIES})

src/external/nexus/examples/hdf5/cmake/config.h.in

@@ -0,0 +1,5 @@
+// config.h
+
+#define PACKAGE_VERSION "@PROJECT_VERSION@"
+#define BUILD_TYPE "@CMAKE_BUILD_TYPE@"
+

src/external/nexus/examples/hdf5/cmake/git-revision.h.in

@@ -0,0 +1,8 @@
+#ifndef GIT_VERSION_H
+#define GIT_VERSION_H
+
+#define GIT_BRANCH "@GIT_BRANCH@"
+#define GIT_CURRENT_SHA1 @GIT_CURRENT_SHA1@
+
+#endif // GIT_VERSION_H
+

src/external/nexus/examples/hdf5/docu/README.md

@@ -0,0 +1,55 @@
+# h5nexus Documentation
+
+This directory contains documentation for the h5nexus project.
+
+## Available Documentation
+
+- **Usage.md** - Comprehensive usage guide with detailed examples and workflow patterns
+
+## Project Structure
+
+The h5nexus example project has the following structure:
+
+```
+h5nexus/
+├── CMakeLists.txt          - Build configuration
+├── main.cpp                - Main program source
+├── git_revision.sh         - Git revision header generator
+├── cmake/
+│   ├── config.h.in         - CMake config template
+│   └── git-revision.h.in   - Git revision template
+└── docu/
+    ├── README.md           - This file
+    └── Usage.md            - Detailed usage documentation
+```
+
+## Building
+
+```bash
+mkdir build
+cd build
+cmake ..
+make
+```
+
+### Prerequisites
+
+- CMake >= 3.26
+- C++17 compatible compiler
+- HDF5 C++ library
+- ROOT >= 6.36 with Minuit2
+
+## Key Classes
+
+The h5nexus example uses the PNeXus library which provides:
+
+- `nxH5::PNeXus` - Main NeXus file reader/writer class
+- `nxH5::PNXdata<T>` - Template class for dataset storage
+- `nxH5::PNeXusDeadTime` - Dead time correction calculator
+- `nxs::checkHDFType()` - File format detection
+
+## Additional Resources
+
+- [Doxygen Manual](https://www.doxygen.nl/manual/)
+- [HDF5 Documentation](https://portal.hdfgroup.org/documentation/)
+- [NeXus Format](https://www.nexusformat.org/)

src/external/nexus/examples/hdf5/git_revision.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+echo "-- Generating header for git hash"
+GIT_HEADER="git-revision.h"
+[ -d src ] || mkdir src
+
+GIT_BRANCH=`git rev-parse --abbrev-ref HEAD`
+
+GIT_VERSION=`git log -n 1 --pretty=format:"%ad - %h"`
+if [ "$(grep -ics "$GIT_VERSION" $GIT_HEADER)" = 1 ] 
+then
+   echo "-- No need to generate new $GIT_HEADER - git hash is unchanged"
+   exit 0;
+fi
+
+echo "-- git branch is  : " $GIT_BRANCH
+echo "-- git version is : " $GIT_VERSION
+
+echo "#ifndef GIT_VERSION_H" > $GIT_HEADER
+echo "#define GIT_VERSION_H" >> $GIT_HEADER
+echo "" >> $GIT_HEADER
+echo "#define GIT_BRANCH \"$GIT_BRANCH\"" >> $GIT_HEADER
+echo "#define GIT_CURRENT_SHA1 \"$GIT_VERSION\"" >> $GIT_HEADER
+echo "" >> $GIT_HEADER
+echo "#endif //GIT_VERSION_H" >> $GIT_HEADER
+
+echo "-- file is generated into" $GIT_HEADER

src/external/nexus/examples/hdf5/main.cpp

@@ -0,0 +1,572 @@
+/***************************************************************************
+
+  main.cpp
+
+  Author: Andreas Suter
+  e-mail: andreas.suter@psi.ch
+
+***************************************************************************/
+
+/***************************************************************************
+ *   Copyright (C) 2007-2026 by Andreas Suter                              *
+ *   andreas.suter@psi.ch                                                  *
+ *                                                                         *
+ *   This program is free software; you can redistribute it and/or modify  *
+ *   it under the terms of the GNU General Public License as published by  *
+ *   the Free Software Foundation; either version 2 of the License, or     *
+ *   (at your option) any later version.                                   *
+ *                                                                         *
+ *   This program is distributed in the hope that it will be useful,       *
+ *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
+ *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
+ *   GNU General Public License for more details.                          *
+ *                                                                         *
+ *   You should have received a copy of the GNU General Public License     *
+ *   along with this program; if not, write to the                         *
+ *   Free Software Foundation, Inc.,                                       *
+ *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
+ ***************************************************************************/
+
+/**
+ * @file main.cpp
+ * @brief Command-line interface for the h5nexus NeXus HDF5 file reader/writer
+ *
+ * This file contains the main() function and command-line interface for the
+ * h5nexus program. It provides functionality to:
+ * - Read and display NeXus HDF5 files
+ * - Write NeXus HDF5 files using the PNXdata approach
+ * - Calculate dead time corrections for muon detector data
+ *
+ * **Command-Line Options:**
+ * - --fn <file>: Input NeXus HDF5 file (required)
+ * - --out <file>: Output NeXus HDF5 file (optional)
+ * - --debug, -d: Enable debug output
+ * - --dead_time_estimate, -dt: Calculate dead time corrections
+ * - --help, -h: Display help message
+ * - --version, -v: Display version information
+ *
+ * @author Andreas Suter
+ * @date 2007-2026
+ * @copyright GNU General Public License v2
+ * @version 1.0
+ *
+ * @see nxH5::PNeXus
+ * @see nxH5::PNeXusDeadTime
+ */
+
+#include <cstring>
+#include <iostream>
+#include <string>
+#include <memory>
+#include <ctime>
+#include <fstream>
+
+#include "hdf5.h"
+
+#include "PNeXus.h"
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#ifdef HAVE_GIT_REV_H
+#include "git-revision.h"
+#endif
+
+//-----------------------------------------------------------------------------
+/**
+ * @brief Display command-line syntax and help information
+ *
+ * Prints the usage syntax and available command-line options for the h5nexus
+ * program to stdout and exits the program.
+ */
+void h5nexus_syntax() {
+  std::cout << std::endl;
+  std::cout << "usage: h5nexus [--help | -h] |" << std::endl;
+  std::cout << "               [--version | -v] |" << std::endl;
+  std::cout << "               --fn <fln> [--debug | -d]" << std::endl;
+  std::cout << "               [--dead_time_estimate | -dt]]" << std::endl;
+  std::cout << "               [--out <fout>]" << std::endl;
+  std::cout << "               [--data idx <dout>]" << std::endl;
+  std::cout << std::endl;
+  std::cout << "options:" << std::endl;
+  std::cout << "  --help, -h: this help." << std::endl;
+  std::cout << "  --version, -v: version of h5nexus." << std::endl;
+  std::cout << "  --fn <fln>: nexus hdf5 input file name <fn>." << std::endl;
+  std::cout << "  --dead_time_estimate, -dt: dead time estimate for the read hdf5 nexus file." << std::endl;
+  std::cout << "  --debug, -d: print additional debug information." << std::endl;
+  std::cout << "  --out <fout>: write the required datasets of a nexus hdf5 file to file " << std::endl;
+  std::cout << "                with name <fout>. Only makes sense together with the option --fn <fln>." << std::endl;
+  std::cout << "  --data idx <dout>: write a single ascii data set with idx to <dout>." << std::endl;
+  std::cout << "                Only makes sense together with the option --fn <fln>." << std::endl;
+  std::cout << std::endl;
+  exit(0);
+}
+
+//-----------------------------------------------------------------------------
+/**
+ * @brief Calculate dead time corrections for muon detector data
+ *
+ * Estimates dead time corrections for each detector in the NeXus file using
+ * the PNeXusDeadTime class and ROOT Minuit2 minimization.
+ *
+ * @param nxs Pointer to the PNeXus object containing the data
+ * @param debug If true, print additional debug information
+ *
+ * @see nxH5::PNeXusDeadTime
+ */
+std::vector<float> h5nexus_deadTimeEstimate(const nxH5::PNeXus *nxs, bool debug)
+{
+  if (debug) {
+    std::cout << std::endl;
+    std::cout << std::endl << "+++++++++++++++++++";
+    std::cout << std::endl << "in deadTimeEstimate";
+    std::cout << std::endl << "+++++++++++++++++++";
+    std::cout << std::endl;
+  }
+
+  nxH5::PNeXusDeadTime ndt(nxs, debug);
+  auto dims = ndt.GetDimensions();
+  for (unsigned int i=0; i<dims[1]; i++) {
+    ndt.minimize(i);
+  }
+
+  return ndt.GetDeadTimeEstimated();
+}
+
+//-----------------------------------------------------------------------------
+void h5nexus_writeData(const nxH5::PNeXus *nxs, const std::string& fln, const std::string& dataOutFln, const int idx, const std::vector<float> dte)
+{
+  std::cout << std::endl << "as35> in h5nexus_writeData: idf version: " << nxs->GetIdfVersion();
+  std::vector<int> counts;
+  std::vector<float> dt;
+  std::vector<long long unsigned int> dims;
+  float resolution{0.0};
+  int good_frames{0};
+
+  if (nxs->GetIdfVersion() == 1) {
+    if (nxs->HasDataset("/run/histogram_data_1/counts")) {
+      std::cout << std::endl << "as35> found counts in idf version 1";
+    }
+  } else {
+    auto dataMap = nxs->GetDataMap();
+    if (nxs->HasDataset("/raw_data_1/detector_1/counts")) {
+        std::cout << std::endl << "as35> found counts in idf version 2";
+      auto counts_data = std::any_cast<nxH5::PNXdata<int>>(dataMap["/raw_data_1/detector_1/counts"]);
+      counts = counts_data.GetData();
+      auto dd = counts_data.GetDimensions();
+      for (auto i=0; i<dd.size(); i++)
+        dims.push_back(dd[i]);
+
+      std::cout << std::endl << "as35> dims: " << dims.size() << ": ";
+      for (auto i=0; i<dims.size(); i++)
+        std::cout << dims[i] << ", ";
+    }
+    if (idx >= dims[1]) {
+      std::cerr << std::endl << "**ERROR** idx=" << idx << " is >= number of dataset=" << dims[1] << std::endl;
+      return;
+    }
+    if (nxs->HasDataset("/raw_data_1/detector_1/dead_time")) {
+      std::cout << std::endl << "as35> found dead_time in idf version 2";
+      auto dt_data = std::any_cast<nxH5::PNXdata<float>>(dataMap["/raw_data_1/detector_1/dead_time"]);
+      dt = dt_data.GetData();
+    }
+    if (nxs->HasDataset("/raw_data_1/instrument/detector_1/resolution")) {
+      std::cout << std::endl << "as35> found resolution in idf version 2";
+      auto r_data = std::any_cast<nxH5::PNXdata<int>>(dataMap["/raw_data_1/instrument/detector_1/resolution"]);
+      auto rr = r_data.GetData();
+      resolution = (float)rr[0];
+      if (r_data.HasAttribute("units")) {
+        std::string units = std::any_cast<std::string>(r_data.GetAttribute("units"));
+        if (units == "picoseconds")
+          resolution *= 1.0e-6;
+        else if (units == "nanoseconds")
+          resolution *= 1.0e-3;
+      }
+    }
+    if (nxs->HasDataset("/raw_data_1/good_frames")) {
+      std::cout << std::endl << "as35> found good_frames in idf version 2";
+      auto gf_data = std::any_cast<nxH5::PNXdata<int>>(dataMap["/raw_data_1/good_frames"]);
+      good_frames = gf_data.GetData()[0];
+    }
+  }
+  std::cout << std::endl;
+
+  float dtei;
+  if (dte.size() > idx)
+    dtei = dte[idx];
+
+  // write dataset
+  std::ofstream fout(dataOutFln);
+  fout << "# NeXus fln: " << fln << std::endl;
+  fout << "# idx=" << idx << std::endl;
+  fout << "# resolution  : " << resolution << " (us)" << std::endl;
+  fout << "# good_frames : " << good_frames << std::endl;
+  fout << "# dead_time   : " << dt[idx] << " (us) : from file" << std::endl;
+  fout << "# dead_time   : " << dtei << " (us) : from estimater" << std::endl;
+  fout << "# ------" << std::endl;
+  fout << "# raw counts, dead time corrected counts (file), dead time corrected counts (estimated)" << std::endl;
+  int cc{0}, dtcc{0}, dtecc{0};
+  // see https://docs.mantidproject.org/v3.9.0/algorithms/ApplyDeadTimeCorr-v1.html#algm-applydeadtimecorr
+  for (auto i=0; i<dims[2]; i++) {
+    cc = counts[i + idx*dims[2]];
+    dtcc = (int)((float)cc / (1.0 - (float)cc * (dt[idx]/(resolution*(float)good_frames))));
+    dtecc = (int)((float)cc / (1.0 - (float)cc * (dtei/(resolution*(float)good_frames))));
+    fout << cc << ", " << dtcc << ", " << dtecc << std::endl;
+  }
+  fout.close();
+}
+
+//-----------------------------------------------------------------------------
+/**
+ * @brief Write NeXus HDF5 file using the PNXdata approach
+ *
+ * Writes all datasets from the PNeXus data map to a new NeXus HDF5 file.
+ * This function uses the WriteNexusFile() method to create a complete
+ * NeXus file with all groups, datasets, and attributes.
+ *
+ * @param nxs Pointer to the PNeXus object containing the data to write
+ * @param outFileName Output filename for the NeXus HDF5 file
+ * @param debug If true, print additional debug information
+ *
+ * @note Currently only supports IDF version 2 files
+ *
+ * @see nxH5::PNeXus::WriteNexusFile()
+ */
+void h5nexus_writeTest(const nxH5::PNeXus *nxs, const std::string& outFileName, bool debug)
+{
+  if (debug) {
+    std::cout << std::endl;
+    std::cout << "++++++++++++++++++++" << std::endl;
+    std::cout << "Writing NeXus file" << std::endl;
+    std::cout << "++++++++++++++++++++" << std::endl;
+    std::cout << std::endl;
+  }
+
+  if (nxs->GetIdfVersion() == 1) {
+    std::cerr << "Error: IDF v1 write not yet implemented" << std::endl;
+    return;
+  }
+
+  // Write using the read object's data
+  int result = const_cast<nxH5::PNeXus*>(nxs)->WriteNexusFile(outFileName, nxs->GetIdfVersion());
+
+  if (result == 0) {
+    std::cout << "Successfully wrote: " << outFileName << std::endl;
+  } else {
+    std::cerr << "Failed to write file: " << outFileName << std::endl;
+  }
+
+  // write data from scratch
+
+  std::unique_ptr<nxH5::PNeXus> nxs_out = std::make_unique<nxH5::PNeXus>();
+
+  std::vector<int> ival;
+  std::vector<float> fval;
+  std::vector<std::string> sval;
+
+  H5::StrType strType(H5::PredType::C_S1, H5T_VARIABLE);
+
+  // ----------
+  // raw_data_1
+  // ----------
+
+  // IDF version
+  ival.push_back(2);
+  nxs_out->AddDataset<int>("/raw_data_1/IDF_version", ival, {1}, H5::PredType::NATIVE_INT);
+  ival.clear();
+
+  // add group attribute to '/raw_data_1'
+  nxs_out->AddGroupAttribute("/raw_data_1", "NX_class", std::string("NXentry"));
+
+  // beamline
+  sval.push_back("piE3");
+  nxs_out->AddDataset<std::string>("/raw_data_1/beamline", sval, {1}, strType);
+  sval.clear();
+
+  // definition
+  sval.push_back("muonTD");
+  nxs_out->AddDataset<std::string>("/raw_data_1/definition", sval, {1}, strType);
+  sval.clear();
+
+  // run_number
+  ival.push_back(1234);
+  nxs_out->AddDataset<int>("/raw_data_1/run_number", ival, {1}, H5::PredType::NATIVE_INT);
+  ival.clear();
+
+  // title
+  sval.push_back("this is the run title.");
+  nxs_out->AddDataset<std::string>("/raw_data_1/title", sval, {1}, strType);
+  sval.clear();
+
+  // start time
+  sval.push_back("2026-01-01T01:02:03");
+  nxs_out->AddDataset<std::string>("/raw_data_1/start_time", sval, {1}, strType);
+  sval.clear();
+
+  // end time
+  sval.push_back("2026-01-01T02:03:42");
+  nxs_out->AddDataset<std::string>("/raw_data_1/end_time", sval, {1}, strType);
+  sval.clear();
+
+  // experiment_identifier - pgroup for PSI
+  sval.push_back("p18324");
+  nxs_out->AddDataset<std::string>("/raw_data_1/experiment_identifier", sval, {1}, strType);
+  sval.clear();
+
+  // -------------------
+  // detector_1 (NXdata)
+  // -------------------
+
+  // add group attribute to /raw_data_1/instrument
+  nxs_out->AddGroupAttribute("/raw_data_1/detector_1", "NX_class", std::string("NXdata"));
+
+  // counts
+  std::vector<int> counts(16*66000, 42); // data 16 histos with length 66000
+  nxs_out->AddDataset<int>("/raw_data_1/detector_1/counts", counts, {1, 16, 66000}, H5::PredType::NATIVE_INT);
+
+  // attributes for counts
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "signal", 1);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "axes", std::string("period_index,spectrum_index,raw_time"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "long_name", std::string("positron_counts"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "t0_bin", 2741);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "first_good_bin", 2741);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "last_good_bin", 66000);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "units", std::string("counts"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "target", std::string("/raw_data_1/instrument/detector_1/counts"));
+
+  // raw_time
+  std::vector<float> raw_time(66000, 0.0);
+  for (unsigned int i=0; i<raw_time.size(); i++)
+    raw_time[i] = 0.1953125f*1.0e-3*((float)i-2741.0f+0.5f);
+  nxs_out->AddDataset<float>("/raw_data_1/detector_1/raw_time", raw_time, {66000}, H5::PredType::NATIVE_FLOAT);
+
+  // attributes raw_time
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/detector_1/raw_time", "units", std::string("microseconds"));
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/detector_1/raw_time", "target", std::string("/raw_data_1/instrument/detector_1/raw_time"));
+
+
+  // ----------
+  // instrument
+  // ----------
+
+  // add group attribute to /raw_data_1/instrument
+  nxs_out->AddGroupAttribute("/raw_data_1/instrument", "NX_class", std::string("NXinstrument"));
+
+  // name
+  sval.push_back("LEM");
+  nxs_out->AddDataset<std::string>("/raw_data_1/instrument/name", sval, {1}, strType);
+  sval.clear();
+
+  // ------
+  // source
+  // ------
+
+  // add group attribute to /raw_data_1/instrument/source
+  nxs_out->AddGroupAttribute("/raw_data_1/instrument/source", "NX_class", std::string("NXsource"));
+
+  // name
+  sval.push_back("PSI");
+  nxs_out->AddDataset<std::string>("/raw_data_1/instrument/source/name", sval, {1}, strType);
+  sval.clear();
+
+  // type
+  sval.push_back("continuous muon source");
+  nxs_out->AddDataset<std::string>("/raw_data_1/instrument/source/types", sval, {1}, strType);
+  sval.clear();
+
+  // probe
+  sval.push_back("postive muons");
+  nxs_out->AddDataset<std::string>("/raw_data_1/instrument/source/probe", sval, {1}, strType);
+  sval.clear();
+
+  // -----------------------
+  // detector_1 (NXdetector)
+  // -----------------------
+
+  // add group attribute to /raw_data_1/instrument/detector_1
+  nxs_out->AddGroupAttribute("/raw_data_1/instrument/detector_1", "NX_class", std::string("NXdetector"));
+
+  // counts
+  nxs_out->AddDataset<int>("/raw_data_1/instrument/detector_1/counts", counts, {1, 16, 66000}, H5::PredType::NATIVE_INT);
+
+  // attributes for counts
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "signal", 1);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "axes", std::string("period_index,spectrum_index,raw_time"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "long_name", std::string("positron_counts"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "t0_bin", 2741);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "first_good_bin", 2741);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "last_good_bin", 66000);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "units", std::string("counts"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "target", std::string("/raw_data_1/instrument/detector_1/counts"));
+
+  // raw_time
+  nxs_out->AddDataset<float>("/raw_data_1/instrument/detector_1/raw_time", raw_time, {66000}, H5::PredType::NATIVE_FLOAT);
+
+  // attributes raw_time
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/raw_time", "units", std::string("microseconds"));
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/raw_time", "target", std::string("/raw_data_1/instrument/detector_1/raw_time"));
+
+  // resolution
+  fval.push_back(195.3125);
+  nxs_out->AddDataset<float>("/raw_data_1/instrument/detector_1/resolution", fval, {1}, H5::PredType::NATIVE_FLOAT);
+  fval.clear();
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/resolution",
+                                      "units", std::string("picoseconds"));
+
+  // spectrum_index
+  for (unsigned int i=0; i<16; i++)
+    ival.push_back(i+1);
+  nxs_out->AddDataset<int>("/raw_data_1/instrument/detector_1/spectrum_index", ival, {16}, H5::PredType::NATIVE_INT);
+  ival.clear();
+
+  // dead_time
+  std::vector<float> deadTime(16, 0.0);
+  nxs_out->AddDataset<float>("/raw_data_1/instrument/detector_1/dead_time", deadTime, {16}, H5::PredType::NATIVE_FLOAT);
+
+  // attributes dead_time
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/dead_time", "available", 0);
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/dead_time", "units", std::string("microseconds"));
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/dead_time", "target", std::string("/raw_data_1/instrument/detector_1/dead_time"));
+
+  // add root attributes
+  // file name
+  nxs_out->AddRootAttribute("file_name", std::string("_test.nxs"));
+  // date-time
+  std::time_t time = std::time({});
+  char timeString[std::size("yyyy-mm-ddThh:mm:ssZ")];
+  std::strftime(std::data(timeString), std::size(timeString),
+                 "%FT%TZ", std::gmtime(&time));
+  nxs_out->AddRootAttribute("file_time", std::string(timeString));
+  // NeXus version
+  nxs_out->AddRootAttribute("NeXus_Version", std::string("4.3.0"));
+  // hdf5 version
+  nxs_out->AddRootAttribute("HDF5_Version", std::string(nxs->GetHdf5Version()));
+  // creator
+  nxs_out->AddRootAttribute("creator", std::string("h5nexus - PSI"));
+
+  nxs_out->WriteNexusFile("_test.nxs");
+}
+
+//-----------------------------------------------------------------------------
+/**
+ * @brief Main entry point for the h5nexus program
+ *
+ * Parses command-line arguments and performs the requested operations:
+ * - Read and display NeXus HDF5 file information
+ * - Write NeXus HDF5 files with modified data
+ * - Calculate dead time corrections
+ *
+ * @param argc Number of command-line arguments
+ * @param argv Array of command-line argument strings
+ *
+ * @return 0 on success, non-zero on error
+ *
+ * @see h5nexus_syntax() for available command-line options
+ */
+int main(int argc, char *argv[])
+{
+  std::string fileName{""};
+  std::string fileNameOut{""};
+  std::string dataNameOut{""};
+  int idx{-1};
+  bool printDebug{false};
+  bool deadTimeEstimate{false};
+
+  if (argc == 1)
+    h5nexus_syntax();
+
+  for (int i=1; i<argc; i++) {
+    if (!strcmp(argv[i], "-h") || !strcmp(argv[i], "--help")) {
+      h5nexus_syntax();
+    } else if (!strcmp(argv[i], "-v") || !strcmp(argv[i], "--version")) {
+#ifdef HAVE_CONFIG_H
+#ifdef HAVE_GIT_REV_H
+      std::cout << std::endl << "h5nexus version: " << PACKAGE_VERSION << ", git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << " (" << BUILD_TYPE << ")" << std::endl << std::endl;
+#else
+      std::cout << std::endl << "h5nexus version: " << PACKAGE_VERSION << " (" << BUILD_TYPE << ")" << std::endl << std::endl;
+#endif
+#else
+#ifdef HAVE_GIT_REV_H
+      std::cout << std::endl << "h5nexus git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << std::endl << std::endl;
+#else
+      std::cout << std::endl << "h5nexus version: unkown." << std::endl << std::endl;
+#endif
+#endif
+      return 0;
+    } else if (!strcmp(argv[i], "--fn")) {
+      if (i+1 >= argc) {
+        std::cout << std::endl << "**ERROR** found --fn without <fln>." << std::endl;
+        h5nexus_syntax();
+      }
+      i++;
+      fileName = argv[i];
+    } else if (!strcmp(argv[i], "-dt") || !strcmp(argv[i], "--dead_time_estimate")) {
+      deadTimeEstimate = true;
+    } else if (!strcmp(argv[i], "-d") || !strcmp(argv[i], "--debug")) {
+        printDebug = true;
+    } else if (!strcmp(argv[i], "--data")) {
+      if (i+2 >= argc) {
+        std::cout << std::endl << "**ERROR** in --data idx <dout>." << std::endl;
+        h5nexus_syntax();
+      }
+      int ii;
+      try {
+        ii = std::stoi(argv[i+1]);
+      } catch (const std::invalid_argument& ia) {
+        std::cout << std::endl << "**ERROR** couldn't convert idx from arguments given." << std::endl;
+        h5nexus_syntax();
+      }
+      if (ii < 0) {
+        std::cout << std::endl << "**ERROR** found idx < 0, namely " << ii << std::endl;
+        h5nexus_syntax();
+      }
+      idx = ii;
+      dataNameOut = argv[i+2];
+      i += 2;
+    } else if (!strcmp(argv[i], "--out")) {
+      if (i+1 >= argc) {
+        std::cout << std::endl << "**ERROR** found --out without <fout>." << std::endl;
+        h5nexus_syntax();
+      }
+      i++;
+      fileNameOut = argv[i];
+    } else {
+      h5nexus_syntax();
+    }
+  }
+  
+  if (fileName.empty()) {
+    std::cerr << std::endl;
+    std::cerr << "**ERROR** <fln> is missing." << std::endl;
+    std::cerr << std::endl;
+    h5nexus_syntax();
+  }
+
+  if (printDebug) {
+    std::cout << std::endl;
+    std::cout << ">> fln  = '" << fileName << "'" << std::endl;
+    std::cout << ">> fout = '" << fileNameOut << "'" << std::endl;
+    std::cout << ">> dout = '" << dataNameOut << "', idx=" << idx << std::endl;
+    std::cout << std::endl;
+  }
+
+  std::unique_ptr<nxH5::PNeXus> nxs = std::make_unique<nxH5::PNeXus>(fileName, printDebug);
+
+  nxs->Dump();
+
+  std::vector<float> dte;
+  if (deadTimeEstimate) {
+    dte = h5nexus_deadTimeEstimate(nxs.get(), printDebug);
+  }
+
+  if (!fileNameOut.empty()) {
+    h5nexus_writeTest(nxs.get(), fileNameOut, printDebug);
+  }
+
+  if (!dataNameOut.empty()) {
+    h5nexus_writeData(nxs.get(), fileName, dataNameOut, idx, dte);
+  }
+
+  return 0;
+}

src/include/PMusr.h

@@ -872,6 +872,9 @@ 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(); }
     virtual PRawRunDataSet* GetDataSet(const UInt_t idx, Bool_t wantHistoNo = true);
     virtual const PDoubleVector* GetDataBin(const UInt_t histoNo) { return fData.GetData(histoNo); }
@@ -913,45 +916,49 @@ class PRawRunData {
     virtual void SetRingAnode(const UInt_t idx, const Double_t dval);
     virtual void SetTimeResolution(const Double_t dval) { fTimeResolution = dval; }
     virtual void SetRedGreenOffset(PIntVector &ivec) { fRedGreenOffset = ivec; }
+    virtual void SetNumberOfGoodFrames(Int_t ival) { fNumberOfGoodFrames = ival; }
+    virtual void SetDeadTimeParam(std::vector<float> dvec) { fDeadTimeParam = dvec; }
     virtual void SetDataSet(PRawRunDataSet &dataSet, UInt_t idx=-1) { fData.Set(dataSet, idx); }
 
     PNonMusrRawRunData fDataNonMusr; ///< keeps all ascii- or db-file info in case of nonMusr fit
 
   private:
-    TString fVersion;                ///< keeps the version information of the data file
+    TString fVersion{"n/a"};                ///< keeps the version information of the data file
-    TString fGenericValidatorURL;    ///< keeps the generic validator MusrRoot URL
+    TString fGenericValidatorURL{"n/a"};    ///< keeps the generic validator MusrRoot URL
-    TString fSpecificValidatorURL;   ///< keeps the instrument specific validator MusrRoot URL
+    TString fSpecificValidatorURL{"n/a"};   ///< keeps the instrument specific validator MusrRoot URL
-    TString fGenerator;              ///< keeps the data file generator name
+    TString fGenerator{"n/a"};              ///< keeps the data file generator name
-    TString fComment;                ///< keeps the data file comment
+    TString fComment{"n/a"};                ///< keeps the data file comment
-    TString fFileName;               ///< keeps the name of the original data file
+    TString fFileName{"n/a"};               ///< keeps the name of the original data file
-    TString fLaboratory;             ///< keeps the name of the laboratory, e.g. PSI, ISIS, TRIUMF, JPARC
+    TString fLaboratory{"n/a"};             ///< keeps the name of the laboratory, e.g. PSI, ISIS, TRIUMF, JPARC
-    TString fBeamline;               ///< keeps the name of the be beamline, e.g. muE4, piM3.1, ...
+    TString fBeamline{"n/a"};               ///< keeps the name of the be beamline, e.g. muE4, piM3.1, ...
-    TString fInstrument;             ///< keeps the name of the instrument, e.g. LEM, GPS, MUSR, EMU, ...
+    TString fInstrument{"n/a"};             ///< keeps the name of the instrument, e.g. LEM, GPS, MUSR, EMU, ...
-    TString fMuonSource;             ///< keeps the type of muon source, e.g. continous surface beam, pulsed beam, low energy muon beam
+    TString fMuonSource{"n/a"};             ///< keeps the type of muon source, e.g. continous surface beam, pulsed beam, low energy muon beam
-    TString fMuonSpecies;            ///< positive muon or negative muon
+    TString fMuonSpecies{"n/a"};            ///< positive muon or negative muon
-    Double_t fMuonBeamMomentum;      ///< given in MeV/c, for LEM this is the momentum of the secondary beamline and NOT the momentum of the low energy beam
+    Double_t fMuonBeamMomentum{PMUSR_UNDEFINED}; ///< given in MeV/c, for LEM this is the momentum of the secondary beamline and NOT the momentum of the low energy beam
-    Double_t fMuonSpinAngle;         ///< gives the muon spin angle in degrees (reference frame depends on the instrument)
+    Double_t fMuonSpinAngle{PMUSR_UNDEFINED};    ///< gives the muon spin angle in degrees (reference frame depends on the instrument)
-    TString fRunName;                ///< name of the run as found in the msr-file
+    TString fRunName{"n/a"};                ///< name of the run as found in the msr-file
-    Int_t   fRunNumber;              ///< run number
+    Int_t   fRunNumber{-1};                 ///< run number
-    TString fRunTitle;               ///< run title
+    TString fRunTitle{"n/a"};               ///< run title
-    TString fSetup;                  ///< description of the setup of this run
+    TString fSetup{"n/a"};                  ///< description of the setup of this run
-    TString fStartTime;              ///< start time of the run
+    TString fStartTime{"n/a"};              ///< start time of the run
-    TString fStartDate;              ///< start date of the run
+    TString fStartDate{"n/a"};              ///< start date of the run
-    time_t fStartDateTimeSec;        ///< start run given as time_t object
+    time_t fStartDateTimeSec{0};            ///< start run given as time_t object
-    TString fStopTime;               ///< stop time of the run
+    TString fStopTime{"n/a"};               ///< stop time of the run
-    TString fStopDate;               ///< stop date of the run
+    TString fStopDate{"n/a"};               ///< stop date of the run
-    time_t fStopDateTimeSec;         ///< stop run given as time_t object
+    time_t fStopDateTimeSec{0};             ///< stop run given as time_t object
-    TString fCryo;                   ///< name of the cryo
+    TString fCryo{"n/a"};                   ///< name of the cryo
-    TString fSample;                 ///< description of the sample
+    TString fSample{"n/a"};                 ///< description of the sample
-    TString fOrientation;            ///< description of the orientation
+    TString fOrientation{"n/a"};            ///< description of the orientation
-    TString fMagnet;                 ///< name of the sample magnet
+    TString fMagnet{"n/a"};                 ///< name of the sample magnet
-    Double_t fField;                 ///< magnetic field value in (G)
+    Double_t fField{PMUSR_UNDEFINED};       ///< magnetic field value in (G)
     PDoublePairVector fTemp;                ///< measured temperatures and standard deviations during the run
-    Double_t fEnergy;                ///< implantation energy of the muon
+    Double_t fEnergy{PMUSR_UNDEFINED};      ///< implantation energy of the muon
-    Double_t fTransport;             ///< LEM transport settings (Moderator HV)
+    Double_t fTransport{PMUSR_UNDEFINED};   ///< LEM transport settings (Moderator HV)
     PDoubleVector fRingAnode;               ///< LEM ring anode HVs (L,R[,T,B])
-    Double_t fTimeResolution;        ///< time resolution of the run in (ns)
+    Double_t fTimeResolution{PMUSR_UNDEFINED}; ///< time resolution of the run in (ns)
     PIntVector fRedGreenOffset;             ///< keeps the Red/Green offsets
+    std::vector<float> fDeadTimeParam;      ///< dead time parameter vector needed for pulsed sources
+    Int_t fNumberOfGoodFrames{0};           ///< needed to correct dead times at pulsed sources
 
     PRawRunDataVector fData;                ///< keeps the histos together with the histo related properties such as T0, first good bin, etc.
 };
@@ -1050,6 +1057,7 @@ class PMsrGlobalBlock {
     virtual Int_t GetFitRangeOffset(UInt_t idx);
     virtual Int_t GetPacking() { return fPacking; }
     virtual Double_t GetEstimatedAlpha() { return fAlpha; }
+    virtual TString GetDeadTimeCorrection() { return fDeadTimeCorrection; }
 
     virtual void SetGlobalPresent(Bool_t bval) { fGlobalPresent = bval; }
     virtual void SetRRFFreq(Double_t freq, const char *unit);
@@ -1063,6 +1071,7 @@ class PMsrGlobalBlock {
     virtual void SetFitRange(Double_t dval, UInt_t idx);
     virtual void SetFitRangeOffset(Int_t ival, UInt_t idx);
     virtual void SetPacking(Int_t ival) { fPacking = ival; }
+    virtual void SetDeadTimeCorrection(TString str) { fDeadTimeCorrection = str; }
 
   private:
     Bool_t fGlobalPresent;    ///< flag showing if a GLOBAL block is present at all.
@@ -1079,6 +1088,7 @@ class PMsrGlobalBlock {
     Int_t fFitRangeOffset[2]; ///< if fit range is given in bins it can have the form fit fgb+n0 lgb-n1. This variable holds the n0 and n1.
     Int_t fPacking;           ///< packing/rebinning
     Double_t fAlpha;          ///< estimated alpha value from F/B counts
+    TString fDeadTimeCorrection; ///< tells if deadtime correction (pulsed sources) should be applied. Possible value: 'no' (default), 'file', 'estimate'
 };
 
 //-------------------------------------------------------------
@@ -1144,6 +1154,7 @@ class PMsrRunBlock {
     virtual Double_t GetFitRange(UInt_t idx);
     virtual Int_t GetFitRangeOffset(UInt_t idx);
     virtual Int_t GetPacking() { return fPacking; }
+    virtual TString GetDeadTimeCorrection() { return fDeadTimeCorrection; }
     virtual Double_t GetEstimatedAlpha() { return fAlpha; }
     virtual Int_t GetXDataIndex() { return fXYDataIndex[0]; }
     virtual Int_t GetYDataIndex() { return fXYDataIndex[1]; }
@@ -1177,6 +1188,7 @@ class PMsrRunBlock {
     virtual void SetFitRange(Double_t dval, UInt_t idx);
     virtual void SetFitRangeOffset(Int_t ival, UInt_t idx);
     virtual void SetPacking(Int_t ival) { fPacking = ival; }
+    virtual void SetDeadTimeCorrection(TString str) { fDeadTimeCorrection = str; }
     virtual void SetXDataIndex(Int_t ival) { fXYDataIndex[0] = ival; }
     virtual void SetYDataIndex(Int_t ival) { fXYDataIndex[1] = ival; }
     virtual void SetXDataLabel(TString& str) { fXYDataLabel[0] = str; }
@@ -1210,6 +1222,7 @@ class PMsrRunBlock {
     Int_t fFitRangeOffset[2];       ///< if fit range is given in bins it can have the form fit fgb+n0 lgb-n1. This variable holds the n0 and n1.
     Double_t fAlpha;                ///< estimated alpha value from F/B counts
     Int_t fPacking;                 ///< packing/rebinning
+    TString fDeadTimeCorrection; ///< tells if deadtime correction (pulsed sources) should be applied. Possible value: 'no' (default), 'file', 'estimate'
     Int_t fXYDataIndex[2];          ///< used to get the data indices when using db-files (fit type 8)
     TString fXYDataLabel[2];        ///< used to get the indices via labels when using db-files  (fit type 8)
 

src/include/PRunDataHandler.h

@@ -30,6 +30,10 @@
 #ifndef _PRUNDATAHANDLER_H_
 #define _PRUNDATAHANDLER_H_
 
+#include <any>
+#include <iostream>
+#include <string>
+
 #include <TString.h>
 
 #include "PMusr.h"
@@ -432,6 +436,8 @@ class PRunDataHandler
     virtual Bool_t FileExistsCheck(const Bool_t fileName, const Int_t idx);
     virtual Bool_t FileExistsCheck(const TString fileName);
     virtual Bool_t ReadRootFile();
+    template <typename T> Bool_t ReadNexusFileIdf1(T& nxs_file);
+    template <typename T> Bool_t ReadNexusFileIdf2(T& nxs_file);
     virtual Bool_t ReadNexusFile();
     virtual Bool_t ReadWkmFile();
     virtual Bool_t ReadPsiBinFile();
@@ -443,7 +449,7 @@ class PRunDataHandler
 
     virtual Bool_t WriteMusrRootFile(Int_t tag=A2M_MUSR_ROOT_DIR, TString fln="");
     virtual Bool_t WriteRootFile(TString fln="");
-    virtual Bool_t WriteNexusFile(TString fln="");
+    virtual Bool_t WriteNexusFile(TString format, TString fln="");
     virtual Bool_t WriteWkmFile(TString fln="");
     virtual Bool_t WritePsiBinFile(TString fln="");
     virtual Bool_t WriteMudFile(TString fln="");
@@ -464,4 +470,417 @@ class PRunDataHandler
     virtual TString GetYear(Int_t month);
 };
 
+//--------------------------------------------------------------------------
+// ReadNexusFileIdf1 (private)
+//--------------------------------------------------------------------------
+/**
+ * <p>Reads a NeXus file with IDF version 1 format.
+ *
+ * <p>Extracts run metadata (laboratory, beamline, instrument, run title,
+ * run number, temperature, field, sample info, time resolution, start/stop
+ * times) and histogram data from the NeXus file structure.
+ *
+ * @tparam T NeXus file handler type (std::unique_ptr<nxH4::PNeXus> and std::unique_ptr<nxH5::PNeXus>)
+ * @param nxs_file reference to the NeXus file handler
+ *
+ * <b>return:</b>
+ * - true at successful reading,
+ * - otherwise false.
+ */
+template <typename T>
+Bool_t PRunDataHandler::ReadNexusFileIdf1(T& nxs_file)
+{
+  PRawRunData    runData;
+  PRawRunDataSet dataSet;
+  TString str;
+  std::string sstr;
+  Int_t ival;
+  Double_t dval, factor;
+  bool ok;
+
+  // get header information
+
+  // get/set laboratory
+  sstr = "n/a";
+  if (nxs_file->HasDataset("/run/lab"))
+    sstr = nxs_file->template GetDataset<std::string>("/run/lab").GetData()[0];
+  runData.SetLaboratory(sstr);
+
+  // get/set beamline
+  sstr = "n/a";
+  if (nxs_file->HasDataset("/run/beamline"))
+    sstr = nxs_file->template GetDataset<std::string>("/run/beamline").GetData()[0];
+  runData.SetBeamline(sstr);
+
+  // get/set instrument
+  sstr = "n/a";
+  if (nxs_file->HasDataset("/run/instrument/name"))
+    sstr = nxs_file->template GetDataset<std::string>("/run/instrument/name").GetData()[0];
+  runData.SetInstrument(sstr);
+
+  // get/set run title
+  str = "n/a";
+  if (nxs_file->HasDataset("/run/title"))
+    sstr = nxs_file->template GetDataset<std::string>("/run/title").GetData()[0];
+  runData.SetRunTitle(sstr);
+
+  // get/set run number
+  ival = -1;
+  if (nxs_file->HasDataset("/run/number"))
+    ival = nxs_file->template GetDataset<int>("/run/number").GetData()[0];
+  runData.SetRunNumber(ival);
+
+  // get/set temperature
+  dval = PMUSR_UNDEFINED;
+  sstr = "n/a";
+  if (nxs_file->HasDataset("/run/sample/temperature")) {
+    auto tmp_ds = nxs_file->template GetDataset<float>("/run/sample/temperature");
+    dval = tmp_ds.GetData()[0];
+    if (tmp_ds.HasAttribute("units"))
+      sstr = std::any_cast<std::string>(tmp_ds.GetAttribute("units"));
+    if (sstr == "Celcius")
+      dval += 273.16;
+  }
+  runData.SetTemperature(0, dval, 0.0);
+
+  // get/set field
+  dval = PMUSR_UNDEFINED;
+  sstr = "n/a";
+  factor = 1.0;
+  if (nxs_file->HasDataset("/run/sample/magnetic_field")) {
+    auto mag_ds = nxs_file->template GetDataset<float>("/run/sample/magnetic_field");
+    dval = mag_ds.GetData()[0];
+    if (mag_ds.HasAttribute("units"))
+      sstr = std::any_cast<std::string>(mag_ds.GetAttribute("units"));
+    if (sstr == "Tesla")
+      factor = 1.0e4;
+  }
+  runData.SetField(dval*factor);
+
+  // get/set implantation energy
+  runData.SetEnergy(PMUSR_UNDEFINED);
+
+  // get/set moderator HV
+  runData.SetTransport(PMUSR_UNDEFINED);
+
+  // get/set RA HV's (LEM specific)
+  for (UInt_t i=0; i<4; i++)
+    runData.SetRingAnode(i, PMUSR_UNDEFINED);
+
+  // get/set setup
+  sstr = "n/a";
+  if (nxs_file->HasDataset("/run/notes"))
+    sstr = nxs_file->template GetDataset<std::string>("/run/notes").GetData()[0];
+  runData.SetSetup(sstr);
+
+  // get/set sample
+  sstr = "n/a";
+  if (nxs_file->HasDataset("/run/sample/name"))
+    sstr = nxs_file->template GetDataset<std::string>("/run/sample/name").GetData()[0];
+  runData.SetSample(sstr);
+
+  // get/set orientation
+  runData.SetOrientation("??");
+
+  // get/set time resolution (ns)
+  dval = PMUSR_UNDEFINED;
+  sstr = "n/a";
+  factor = 1.0;
+  if (nxs_file->HasDataset("/run/histogram_data_1/resolution")) {
+    auto res_ds = nxs_file->template GetDataset<int>("/run/histogram_data_1/resolution");
+    dval = res_ds.GetData()[0];
+    if (res_ds.HasAttribute("units"))
+      sstr = std::any_cast<std::string>(res_ds.GetAttribute("units"));
+    if ((sstr == "picoseconds") || (sstr == "pico.seconds"))
+      factor = 1.0e-3; // ps -> ns
+  }
+  runData.SetTimeResolution(dval*factor);
+
+  // get/set start/stop time
+  sstr = "n/a";
+  TString date{"n/a"}, time{"n/a"};
+  if (nxs_file->HasDataset("/run/start_time"))
+    sstr = nxs_file->template GetDataset<std::string>("/run/start_time").GetData()[0];
+  str = sstr;
+  SplitTimeDate(str, time, date, ok);
+  if (ok) {
+    runData.SetStartTime(time);
+    runData.SetStartDate(date);
+  }
+
+  sstr = "n/a";
+  date = "n/a";
+  time = "n/a";
+  if (nxs_file->HasDataset("/run/stop_time"))
+    sstr = nxs_file->template GetDataset<std::string>("/run/stop_time").GetData()[0];
+  str = sstr;
+  SplitTimeDate(str, time, date, ok);
+  if (ok) {
+    runData.SetStopTime(time);
+    runData.SetStopDate(date);
+  }
+
+  // get/set deadtime relevant parameters
+  if (nxs_file->HasDataset("/run/instrument/detector/deadtimes")) {
+    std::vector<float> dt;
+    dt = nxs_file->template GetDataset<float>("/run/instrument/detector/deadtimes").GetData();
+    runData.SetDeadTimeParam(dt);
+  }
+  if (nxs_file->HasDataset("/run/instrument/beam/frames_good")) {
+    ival = nxs_file->template GetDataset<float>("/run/instrument/beam/frames_good").GetData()[0];
+    runData.SetNumberOfGoodFrames(ival);
+  }
+
+  // data with its metadata
+  if (nxs_file->HasDataset("/run/histogram_data_1/counts")) {
+    int t0_bin{-1}, fgb{-1}, lgb{-1}, noOfHistos{-1}, histoLength{-1};
+    auto count_ds = nxs_file->template GetDataset<int>("/run/histogram_data_1/counts");
+    auto count = count_ds.GetData();
+    // get all necessary attributes
+    if (count_ds.HasAttribute("t0_bin"))
+      t0_bin = std::any_cast<int>(count_ds.GetAttribute("t0_bin"));
+    if (count_ds.HasAttribute("first_good_bin"))
+      fgb = std::any_cast<int>(count_ds.GetAttribute("first_good_bin"));
+    if (count_ds.HasAttribute("last_good_bin"))
+      lgb = std::any_cast<int>(count_ds.GetAttribute("last_good_bin"));
+    if (count_ds.HasAttribute("number"))
+      noOfHistos = std::any_cast<int>(count_ds.GetAttribute("number"));
+    if (count_ds.HasAttribute("length"))
+      histoLength = std::any_cast<int>(count_ds.GetAttribute("length"));
+    if (static_cast<int>(count.size()) != noOfHistos*histoLength) {
+      std::cerr << std::endl << "**ERROR** PNeXus data size error! count.size()=" << count.size() << ", #histos=" << noOfHistos << ", length=" << histoLength << "." << std::endl;
+      return false;
+    }
+    // fill dataSet
+    PDoubleVector data;
+    for (int i=0; i<noOfHistos; i++) {
+      dataSet.Clear();
+      dataSet.SetHistoNo(i+1); // i.e. histo numbers start with 1
+      dataSet.SetTimeZeroBin(t0_bin);
+      dataSet.SetFirstGoodBin(fgb);
+      dataSet.SetLastGoodBin(lgb);
+      for (int j=0; j<histoLength; j++)
+        data.push_back(count[i*histoLength+j]);
+      dataSet.SetData(data);
+      runData.SetDataSet(dataSet);
+      data.clear();
+    }
+
+    // keep run name from the msr-file
+    runData.SetRunName(fRunName);
+
+    // keep the information
+    fData.push_back(runData);
+  } else { // no data found
+    std::cerr << std::endl << "**ERROR** PNeXus couldn't obtain data: '/run/histogram_data_1/counts' is missing." << std::endl;
+    return false;
+  }
+
+  return true;
+}
+
+//--------------------------------------------------------------------------
+// ReadNexusFileIdf2 (private)
+//--------------------------------------------------------------------------
+template <typename T>
+Bool_t PRunDataHandler::ReadNexusFileIdf2(T& nxs_file)
+{
+  PRawRunData    runData;
+  PRawRunDataSet dataSet;
+  TString str;
+  std::string sstr;
+  Int_t ival;
+  Double_t dval, factor;
+  bool ok;
+
+  // get header information
+
+  // get/set laboratory
+  sstr = "n/a";
+  if (nxs_file->HasDataset("/raw_data_1/instrument/source/name"))
+    sstr = nxs_file->template GetDataset<std::string>("/raw_data_1/instrument/source/name").GetData()[0];
+  runData.SetLaboratory(sstr);
+
+  // get/set beamline
+  sstr = "n/a";
+  if (nxs_file->HasDataset("/raw_data_1/instrument/name"))
+    sstr = nxs_file->template GetDataset<std::string>("/raw_data_1/instrument/name").GetData()[0];
+  runData.SetBeamline(sstr);
+  runData.SetBeamline(sstr);
+
+  // get/set muon source
+  sstr = "n/a";
+  if (nxs_file->HasDataset("/raw_data_1/instrument/source/type"))
+    sstr = nxs_file->template GetDataset<std::string>("/raw_data_1/instrument/source/type").GetData()[0];
+  runData.SetMuonSource(sstr);
+
+  // get/set muon species
+  sstr = "n/a";
+  if (nxs_file->HasDataset("/raw_data_1/instrument/source/probe"))
+    sstr = nxs_file->template GetDataset<std::string>("/raw_data_1/instrument/source/probe").GetData()[0];
+  runData.SetMuonSpecies(sstr);
+
+  // get/set run title
+  sstr = "n/a";
+  if (nxs_file->HasDataset("/raw_data_1/title"))
+    sstr = nxs_file->template GetDataset<std::string>("/raw_data_1/title").GetData()[0];
+  runData.SetRunTitle(sstr);
+
+  // get/set run number
+  ival = -1;
+  if (nxs_file->HasDataset("/raw_data_1/run_number"))
+    ival = nxs_file->template GetDataset<int>("/raw_data_1/run_number").GetData()[0];
+  runData.SetRunNumber(ival);
+
+  // get/set temperature
+  dval = PMUSR_UNDEFINED;
+  sstr = "n/a";
+  if (nxs_file->HasDataset("/raw_data_1/sample/temperature")) {
+    auto tmp_ds = nxs_file->template GetDataset<float>("/raw_data_1/sample/temperature");
+    dval = tmp_ds.GetData()[0];
+    if (tmp_ds.HasAttribute("units"))
+      sstr = std::any_cast<std::string>(tmp_ds.GetAttribute("units"));
+    if (sstr == "Celcius")
+      dval += 273.16;
+  }
+  runData.SetTemperature(0, dval, 0.0);
+
+  // get/set field
+  dval = PMUSR_UNDEFINED;
+  sstr = "n/a";
+  factor = 1.0;
+  if (nxs_file->HasDataset("/raw_data_1/sample/magnetic_field")) {
+    auto mag_ds = nxs_file->template GetDataset<float>("/raw_data_1/sample/magnetic_field");
+    dval = mag_ds.GetData()[0];
+    if (mag_ds.HasAttribute("units"))
+      sstr = std::any_cast<std::string>(mag_ds.GetAttribute("units"));
+    if (sstr == "Tesla")
+      factor = 1.0e4;
+  }
+  runData.SetField(dval*factor);
+
+  // get/set implantation energy
+  runData.SetEnergy(PMUSR_UNDEFINED);
+
+  // get/set implantation energy
+  runData.SetEnergy(PMUSR_UNDEFINED);
+
+  // get/set moderator HV
+  runData.SetTransport(PMUSR_UNDEFINED);
+
+  // get/set RA HV's (LEM specific)
+  for (UInt_t i=0; i<4; i++)
+    runData.SetRingAnode(i, PMUSR_UNDEFINED);
+
+  // get/set setup
+  sstr  = "n/a";
+  runData.SetSetup(str);
+
+  // get/set sample
+  sstr = "n/a";
+  if (nxs_file->HasDataset("/raw_data_1/sample/name"))
+    sstr = nxs_file->template GetDataset<std::string>("/raw_data_1/sample/name").GetData()[0];
+  runData.SetSample(sstr);
+
+  // get/set orientation
+  runData.SetOrientation("n/a");
+
+  // get/set time resolution (ns)
+  dval = PMUSR_UNDEFINED;
+  sstr = "n/a";
+  factor = 1.0;
+  if (nxs_file->HasDataset("/raw_data_1/instrument/detector_1/resolution")) {
+    auto res_ds = nxs_file->template GetDataset<int>("/raw_data_1/instrument/detector_1/resolution");
+    dval = res_ds.GetData()[0];
+    if (res_ds.HasAttribute("units"))
+      sstr = std::any_cast<std::string>(res_ds.GetAttribute("units"));
+    if ((sstr == "picoseconds") || (sstr == "pico.seconds"))
+      factor = 1.0e-3; // ps -> ns
+  }
+  runData.SetTimeResolution(dval*factor);
+
+  // get/set start/stop time
+  sstr = "n/a";
+  TString date{"n/a"}, time{"n/a"};
+  if (nxs_file->HasDataset("/raw_data_1/start_time"))
+    sstr = nxs_file->template GetDataset<std::string>("/raw_data_1/start_time").GetData()[0];
+  str = sstr;
+  SplitTimeDate(str, time, date, ok);
+  if (ok) {
+    runData.SetStartTime(time);
+    runData.SetStartDate(date);
+  }
+
+  sstr = "n/a";
+  date = "n/a";
+  time = "n/a";
+  if (nxs_file->HasDataset("/raw_data_1/end_time"))
+    sstr = nxs_file->template GetDataset<std::string>("/raw_data_1/end_time").GetData()[0];
+  str = sstr;
+  SplitTimeDate(str, time, date, ok);
+  if (ok) {
+    runData.SetStopTime(time);
+    runData.SetStopDate(date);
+  }
+
+  // get/set deadtime relevant parameters
+  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/detector_1/dead_time").GetData();
+    runData.SetDeadTimeParam(dt);
+  }
+  if (nxs_file->HasDataset("/raw_data_1/good_frames")) {
+    ival = nxs_file->template GetDataset<int>("/raw_data_1/good_frames").GetData()[0];
+    runData.SetNumberOfGoodFrames(ival);
+  }
+
+  // data with its metadata
+  if (nxs_file->HasDataset("/raw_data_1/instrument/detector_1/counts")) {
+    int t0_bin{-1}, fgb{-1}, lgb{-1}, noOfHistos{-1}, histoLength{-1};
+    auto count_ds = nxs_file->template GetDataset<int>("/raw_data_1/instrument/detector_1/counts");
+    auto count = count_ds.GetData();
+    auto dims = count_ds.GetDimensions();
+    if (dims.size() < 3) {
+      std::cerr << std::endl << "**ERROR** PNeXus data dimension error! dims.size()=" << dims.size() << ", expecting == 3." << std::endl;
+      return false;
+    }
+    noOfHistos = dims[1];
+    histoLength = dims[2];
+    // get all necessary attributes
+    if (count_ds.HasAttribute("t0_bin"))
+      t0_bin = std::any_cast<int>(count_ds.GetAttribute("t0_bin"));
+    if (count_ds.HasAttribute("first_good_bin"))
+      fgb = std::any_cast<int>(count_ds.GetAttribute("first_good_bin"));
+    if (count_ds.HasAttribute("last_good_bin"))
+      lgb = std::any_cast<int>(count_ds.GetAttribute("last_good_bin"));
+    if (static_cast<int>(count.size()) != noOfHistos*histoLength) {
+      std::cerr << std::endl << "**ERROR** PNeXus data size error! count.size()=" << count.size() << ", #histos=" << noOfHistos << ", length=" << histoLength << "." << std::endl;
+      return false;
+    }
+
+    // fill dataSet
+    PDoubleVector data;
+    for (int i=0; i<noOfHistos; i++) {
+      dataSet.Clear();
+      dataSet.SetHistoNo(i+1); // i.e. histo numbers start with 1
+      dataSet.SetTimeZeroBin(t0_bin);
+      dataSet.SetFirstGoodBin(fgb);
+      dataSet.SetLastGoodBin(lgb);
+      for (int j=0; j<histoLength; j++)
+        data.push_back(count[i*histoLength+j]);
+      dataSet.SetData(data);
+      runData.SetDataSet(dataSet);
+      data.clear();
+    }
+
+    // keep run name from the msr-file
+    runData.SetRunName(fRunName);
+
+    // keep the information
+    fData.push_back(runData);
+  }
+
+  return true;
+}
+
 #endif //  _PRUNDATAHANDLER_H_