fix git-revision.h generation: output to build tree and add missing dependencies

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>
generate git-revision.h at build time instead of configure time
2026-01-29 19:52:16 +01:00 · 2026-01-29 19:35:20 +01:00 · 2026-01-26 20:32:34 +01:00 · 2026-01-26 19:52:41 +01:00 · 2026-01-25 14:49:38 +01:00 · 2026-01-25 14:45:46 +01:00
35 changed files with 6688 additions and 13856 deletions
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -6,7 +6,7 @@ if (CMAKE_VERSION GREATER_EQUAL "3.3")
  cmake_policy(SET CMP0167 NEW)
 endif ()  

-project(musrfit VERSION 1.9.11 LANGUAGES C CXX)
+project(musrfit VERSION 1.9.10 LANGUAGES C CXX)

 #--- musrfit specific options -------------------------------------------------
 option(nexus "build optional NeXus support. Needed for ISIS" OFF)
@@ -211,41 +211,14 @@ if (qt_based_tools)
  endif (qt_version STREQUAL 3)
 endif (qt_based_tools)

-#--- if NeXus check also for HDF4 (optional), HDF5 ----------------------------
+#--- if NeXus check also for HDF4, HDF5, and MXML -----------------------------
 if (nexus)
  find_package(HDF5 COMPONENTS CXX REQUIRED)
  if (HAVE_HDF4)
-    #--- 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})
+    find_package(HDF4 REQUIRED)
    add_definitions(-DHAVE_HDF4)
  endif (HAVE_HDF4)  
+  find_package(NEXUS REQUIRED)
  add_definitions(-DPNEXUS_ENABLED)
 endif (nexus)

@@ -350,6 +323,7 @@ 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("")
--- a/cmake/FindHDF4.cmake
+++ b/cmake/FindHDF4.cmake
@@ -0,0 +1,97 @@
+## 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})
--- a/cmake/FindMXML.cmake
+++ b/cmake/FindMXML.cmake
@@ -0,0 +1,34 @@
+# - 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)
+
--- a/cmake/FindNEXUS.cmake
+++ b/cmake/FindNEXUS.cmake
@@ -0,0 +1,45 @@
+# - 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)
+
+
+
--- a/doc/examples/data/EMU00005989_v2.nxs
+++ b/doc/examples/data/EMU00005989_v2.nxs
--- a/doc/examples/data/emu00139040.nxs
+++ b/doc/examples/data/emu00139040.nxs
--- a/doc/examples/test-asy-NeXus2.msr
+++ b/doc/examples/test-asy-NeXus2.msr
@@ -1,32 +1,33 @@
-Ag_T=100_F=20
+nc-ZnO T=80 F=69
 ###############################################################
 FITPARAMETER
 #       No Name        Value     Step        Pos_Error   Boundaries
-        1 alpha       1.02825   -0.00097    0.00098     
-        2 asym        0.23163   -0.00083    0.00103     0       0.3     
-        3 phase       0.000     -0.000      0.011       0       100     
-        4 field       20.310    -0.010      0.010       0       none    
-        5 rate        0.00031   -0.00031    0.00134     0       100     
+        1 alpha       0.88008   -0.00063    0.00063     
+        2 asym        0.1708    -0.0017     0.0017      0       0.3     
+        3 phase       3.90      -0.38       0.38        0       100     
+        4 field       71.003    -0.036      0.036       0       none    
+        5 rate        0.1526    -0.0024     0.0024      0       100     
+        6 beta        1.231     -0.046      0.047       

 ###############################################################
 THEORY
 asymmetry      2
 TFieldCos      3  fun1       (phase frequency)
-simplExpo      5          (rate)
+generExpo      5     6       (rate exponent)

 ###############################################################
 FUNCTIONS
 fun1 = gamma_mu * par4

 ###############################################################
-RUN data/emu00139040 EMU ISIS NEXUS   (name beamline institute data-file-format)
+RUN data/EMU00005989_v2 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         1-48 
-backward        49-96 
+forward         1-16 
+backward        17-32 
 backgr.fix      0           0           
-data            10      2048    10      2048    
+data            40      1500    40      1500    
 fit             0.2     14     
 packing         1

@@ -38,19 +39,19 @@ SAVE

 ###############################################################
 FOURIER
-units            Gauss   # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
+units            Gauss   # units either 'Gauss', 'MHz', or 'Mc/s'
 fourier_power    10
 apodization      STRONG  # NONE, WEAK, MEDIUM, STRONG
-plot             REAL    # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE, PHASE_OPT_REAL
+plot             REAL    # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
 range            0    100
 phase            par2

 ###############################################################
 PLOT 2   (asymmetry plot)
 runs     1   
-range    0   14   -0.32   0.32
-view_packing 10
+range    0   14   -0.22   0.22
+view_packing 5

 ###############################################################
-STATISTIC --- 2026-02-06 14:00:49
-  chisq = 1092.3, NDF = 858, chisq/NDF = 1.273055
+STATISTIC --- 2012-03-20 10:28:41
+  chisq = 796.7, NDF = 846, chisq/NDF = 0.941749
--- a/doc/examples/test-histo-NeXus2.msr
+++ b/doc/examples/test-histo-NeXus2.msr
@@ -1,22 +1,23 @@
-Ag_T=100_F=20
+nc-ZnO T=80 F=69
 ###############################################################
 FITPARAMETER
 #       No Name        Value     Step        Pos_Error   Boundaries
        1 zero        0         0           none        
-        2 phase       0.000000011  -0.000000011 0.005772888 0       100     
-        3 field       20.3391   -0.0085     0.0085      0       none    
-        4 asym        0.23461   -0.00051    0.00051     0       0.3     
-        5 rate        0.0239    -0.0040     0.0035      0       100     
-        6 Norm_L      1151.24   -0.53       0.53        
-        7 BG_L        0         0           none        0       none    
-        8 Norm_R      1178.60   -0.58       0.58        0       none    
-        9 BG_R        0         0           none        0       none    
-       10 relPhase    178.49    -0.20       0.20        0       none    
+        2 phase       2.81      -0.30       0.30        0       100     
+        3 field       70.998    -0.025      0.025       0       none    
+        4 asym        0.1700    -0.0011     0.0012      0       0.3     
+        5 rate        0.1523    -0.0017     0.0017      0       100     
+        6 beta        1.255     -0.033      0.033       
+        7 Norm_L      2410.44   -0.83       0.83        
+        8 BG_L        0         0           none        0       none    
+        9 Norm_R      2121.43   -0.77       0.77        0       none    
+       10 BG_R        0         0           none        0       none    
+       11 relPhase    182.29    -0.31       0.31        0       none    

 ###############################################################
 THEORY
 asymmetry      4
-simpleGss      5          (rate)
+generExpo      5     6       (rate exponent)
 TFieldCos   fun1  fun2       (phase frequency)

 ###############################################################
@@ -27,25 +28,22 @@ fun2 = gamma_mu * par3
 ###############################################################
 GLOBAL
 fittype         0         (single histogram fit)
-data            5       2048    
-t0              10.0    
-deadtime-cor    file
-fit             0.144   30     
+data            40      1500    
+fit             0.2     14     
 packing         1

 ###############################################################
-RUN data/emu00139040 EMU ISIS NEXUS   (name beamline institute data-file-format)
-norm            6
-backgr.fit      7
+RUN data/EMU00005989_v2 XXXX ISIS NEXUS   (name beamline institute data-file-format)
+norm            7
+backgr.fit      8
 map             1    0    0    0    0    0    0    0    0    0
-forward         1-48 
-#deadtime-cor    file
+forward         1-16 

-RUN data/emu00139040 XXXX ISIS NEXUS   (name beamline institute data-file-format)
-norm            8
-backgr.fit      9
-map            10    0    0    0    0    0    0    0    0    0
-forward         49-96 
+RUN data/EMU00005989_v2 XXXX ISIS NEXUS   (name beamline institute data-file-format)
+norm            9
+backgr.fit      10
+map            11    0    0    0    0    0    0    0    0    0
+forward         17-32 

 ###############################################################
 COMMANDS
@@ -61,15 +59,15 @@ 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, par10
+phase            parR2 par11

 ###############################################################
 PLOT 0   (single histo plot)
 lifetimecorrection
 runs        1   2
-range    0   20   -0.35   0.35
-#view_packing 10
+range    0   14   -0.22   0.22
+view_packing 2

 ###############################################################
-STATISTIC --- 2026-02-08 15:32:12
-  maxLH = 4233.1, NDF = 3725, maxLH/NDF = 1.136412
+STATISTIC --- 2019-03-12 18:08:05
+  maxLH = 2585.1, NDF = 1696, maxLH/NDF = 1.524236
--- a/doc/musrfit_dox.cfg
+++ b/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         = 1.9.11
+PROJECT_NUMBER         = 1.9.10

 # 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
@@ -923,18 +923,6 @@ 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 \
@@ -2253,7 +2241,7 @@ 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             = HAVE_HDF4
+PREDEFINED             =

 # 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
--- a/src/classes/CMakeLists.txt
+++ b/src/classes/CMakeLists.txt
@@ -138,7 +138,6 @@ 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
@@ -152,7 +151,6 @@ 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}
--- a/src/classes/PMsrHandler.cpp
+++ b/src/classes/PMsrHandler.cpp
@@ -814,10 +814,6 @@ 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;
        }
@@ -1161,10 +1157,6 @@ 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;
        }
@@ -3342,20 +3334,6 @@ 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
@@ -3953,27 +3931,6 @@ 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)) {

--- a/src/classes/PMusr.cpp
+++ b/src/classes/PMusr.cpp
@@ -721,22 +721,6 @@ 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)
--- a/src/classes/PRunDataHandler.cpp
+++ b/src/classes/PRunDataHandler.cpp
--- a/src/classes/PRunSingleHisto.cpp
+++ b/src/classes/PRunSingleHisto.cpp
@@ -1069,38 +1069,6 @@ 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;
--- a/src/dump_header.cpp
+++ b/src/dump_header.cpp
@@ -37,7 +37,6 @@
 #include <cstring>
 #include <ctime>
 #include <cassert>
-#include <cstddef>

 #include <iostream>
 #include <fstream>
@@ -366,39 +365,15 @@ 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
-  nxs::HDFType type = nxs::checkHDFType(fileName);
+  std::unique_ptr<PNeXus> nxs_file = std::make_unique<PNeXus>(fileName.c_str());

-  // check for type errors, missing enabled HDF4
-  switch (type) {
-    case nxs::HDFType::HDF4:
-      std::cout << std::endl << ">> PRunDataHandler::ReadNexusFile(): HDF4 file." << std::endl;
-#ifndef HAVE_HDF4
-      std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): **ERROR**, HDF4 is not enabled." << std::endl;
+  if (nxs_file->IsValid(false)) {
+    nxs_file->Dump(counts);
+  } else {
+    std::cerr << std::endl;
+    std::cerr << "**ERROR** found invalid NeXus file." << std::endl;
+    std::cerr << 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;
--- a/src/external/nexus/CMakeLists.txt
+++ b/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 "1.0.0")
+set(PNEXUS_VERSION "0.9.0")
 set(PNEXUS_LIBRARY_NAME "PNeXus")
 configure_file("PNeXus.pc.in" "PNeXus.pc" @ONLY)

@@ -28,13 +28,7 @@ target_include_directories(
 )

 #--- add library dependencies -------------------------------------------------
-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})
+target_link_libraries(PNeXus ${NEXUS_LIBRARY})

 #--- install PNeXus solib -----------------------------------------------------
 install(TARGETS PNeXus DESTINATION lib)
--- a/src/external/nexus/PNeXus.cpp
+++ b/src/external/nexus/PNeXus.cpp
--- a/src/external/nexus/PNeXus.h
+++ b/src/external/nexus/PNeXus.h
--- a/src/external/nexus/README.Cygwin
+++ b/src/external/nexus/README.Cygwin
@@ -0,0 +1,69 @@
+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
--- a/src/external/nexus/Usage.md
+++ b/src/external/nexus/Usage.md
--- a/src/external/nexus/examples/hdf4/CMakeLists.txt
+++ b/src/external/nexus/examples/hdf4/CMakeLists.txt
@@ -1,149 +0,0 @@
-# - 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} ${ROOT_LIBRARIES})
--- a/src/external/nexus/examples/hdf4/cmake/config.h.in
+++ b/src/external/nexus/examples/hdf4/cmake/config.h.in
@@ -1,7 +0,0 @@
-/* config.h.in.  Generated from CMakeLists.txt  */
-
-/* Define to 1 if you have the <config.h> file. */
-#cmakedefine HAVE_CONFIG_H @HAVE_CONFIG_H@
-
-/* h4nexus version */
-#define H4NEXUS_VERSION "@h4nexus_VERSION@"
--- a/src/external/nexus/examples/hdf4/docu/README.md
+++ b/src/external/nexus/examples/hdf4/docu/README.md
@@ -1,155 +0,0 @@
-# h4nexus - handle muSR-NeXus files via HDF4 only
-
-## Contents
-
-Tests and classes to handle muSR-NeXus files directly via the HDF4 C API.
-
-This project provides the same API as h5nexus but uses HDF4 instead of HDF5 for handling NeXus files.
-
-## Features
-
- **Read and write NeXus HDF4 files** with a clean C++ API
- **Case-insensitive path lookup** for datasets and groups
- **Type-safe data handling** using template classes
- **Dead time correction calculation** for muon detector data using ROOT Minuit2
- **Compatible API with h5nexus** for easy migration
-
-## Key Classes
-
- `nxH4::PNeXus` - Main class for reading/writing NeXus HDF4 files
- `nxH4::PNXdata<T>` - Template class for storing dataset content with attributes
- `nxH4::PNeXusDeadTime` - Dead time correction calculator for muon detector data
-
-## Requirements
-
- CMake >= 3.26
- C++17 compatible compiler
- HDF4 library (libhdf4-dev or hdf-devel)
- ROOT >= 6.36 with Minuit2 component
- pkg-config
-
-## Building
-
-```bash
-mkdir build
-cd build
-cmake ..
-make
-```
-
-## Installation
-
-```bash
-make install
-```
-
-This will install:
- Library: `libh4nexus.so` in `${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>
--- a/src/external/nexus/examples/hdf4/git_revision.sh
+++ b/src/external/nexus/examples/hdf4/git_revision.sh
@@ -1,35 +0,0 @@
-#!/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"
--- a/src/external/nexus/examples/hdf4/main.cpp
+++ b/src/external/nexus/examples/hdf4/main.cpp
@@ -1,447 +0,0 @@
-/***************************************************************************
-
-  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;
-}
--- a/src/external/nexus/examples/hdf5/CMakeLists.txt
+++ b/src/external/nexus/examples/hdf5/CMakeLists.txt
@@ -1,119 +0,0 @@
-# - 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})
--- a/src/external/nexus/examples/hdf5/cmake/config.h.in
+++ b/src/external/nexus/examples/hdf5/cmake/config.h.in
@@ -1,5 +0,0 @@
-// config.h
-
-#define PACKAGE_VERSION "@PROJECT_VERSION@"
-#define BUILD_TYPE "@CMAKE_BUILD_TYPE@"
-
--- a/src/external/nexus/examples/hdf5/cmake/git-revision.h.in
+++ b/src/external/nexus/examples/hdf5/cmake/git-revision.h.in
@@ -1,8 +0,0 @@
-#ifndef GIT_VERSION_H
-#define GIT_VERSION_H
-
-#define GIT_BRANCH "@GIT_BRANCH@"
-#define GIT_CURRENT_SHA1 @GIT_CURRENT_SHA1@
-
-#endif // GIT_VERSION_H
-
--- a/src/external/nexus/examples/hdf5/docu/README.md
+++ b/src/external/nexus/examples/hdf5/docu/README.md
@@ -1,55 +0,0 @@
-# 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/)
--- a/src/external/nexus/examples/hdf5/docu/Usage.md
+++ b/src/external/nexus/examples/hdf5/docu/Usage.md
--- a/src/external/nexus/examples/hdf5/git_revision.sh
+++ b/src/external/nexus/examples/hdf5/git_revision.sh
@@ -1,27 +0,0 @@
-#!/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
--- a/src/external/nexus/examples/hdf5/main.cpp
+++ b/src/external/nexus/examples/hdf5/main.cpp
@@ -1,572 +0,0 @@
-/***************************************************************************
-
-  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;
-}
--- a/src/external/nexus/nexus_definitions/NeXus-Def-V2-Rev10.pdf
+++ b/src/external/nexus/nexus_definitions/NeXus-Def-V2-Rev10.pdf
--- a/src/include/PMusr.h
+++ b/src/include/PMusr.h
@@ -872,9 +872,6 @@ 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); }
@@ -916,49 +913,45 @@ 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{"n/a"};                ///< keeps the version information of the data file
-    TString fGenericValidatorURL{"n/a"};    ///< keeps the generic validator MusrRoot URL
-    TString fSpecificValidatorURL{"n/a"};   ///< keeps the instrument specific validator MusrRoot URL
-    TString fGenerator{"n/a"};              ///< keeps the data file generator name
-    TString fComment{"n/a"};                ///< keeps the data file comment
-    TString fFileName{"n/a"};               ///< keeps the name of the original data file
-    TString fLaboratory{"n/a"};             ///< keeps the name of the laboratory, e.g. PSI, ISIS, TRIUMF, JPARC
-    TString fBeamline{"n/a"};               ///< keeps the name of the be beamline, e.g. muE4, piM3.1, ...
-    TString fInstrument{"n/a"};             ///< keeps the name of the instrument, e.g. LEM, GPS, MUSR, EMU, ...
-    TString fMuonSource{"n/a"};             ///< keeps the type of muon source, e.g. continous surface beam, pulsed beam, low energy muon beam
-    TString fMuonSpecies{"n/a"};            ///< positive muon or negative muon
-    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{PMUSR_UNDEFINED};    ///< gives the muon spin angle in degrees (reference frame depends on the instrument)
-    TString fRunName{"n/a"};                ///< name of the run as found in the msr-file
-    Int_t   fRunNumber{-1};                 ///< run number
-    TString fRunTitle{"n/a"};               ///< run title
-    TString fSetup{"n/a"};                  ///< description of the setup of this run
-    TString fStartTime{"n/a"};              ///< start time of the run
-    TString fStartDate{"n/a"};              ///< start date of the run
-    time_t fStartDateTimeSec{0};            ///< start run given as time_t object
-    TString fStopTime{"n/a"};               ///< stop time of the run
-    TString fStopDate{"n/a"};               ///< stop date of the run
-    time_t fStopDateTimeSec{0};             ///< stop run given as time_t object
-    TString fCryo{"n/a"};                   ///< name of the cryo
-    TString fSample{"n/a"};                 ///< description of the sample
-    TString fOrientation{"n/a"};            ///< description of the orientation
-    TString fMagnet{"n/a"};                 ///< name of the sample magnet
-    Double_t fField{PMUSR_UNDEFINED};       ///< magnetic field value in (G)
+    TString fVersion;                ///< keeps the version information of the data file
+    TString fGenericValidatorURL;    ///< keeps the generic validator MusrRoot URL
+    TString fSpecificValidatorURL;   ///< keeps the instrument specific validator MusrRoot URL
+    TString fGenerator;              ///< keeps the data file generator name
+    TString fComment;                ///< keeps the data file comment
+    TString fFileName;               ///< keeps the name of the original data file
+    TString fLaboratory;             ///< 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 fInstrument;             ///< 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 fMuonSpecies;            ///< 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 fMuonSpinAngle;         ///< 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
+    Int_t   fRunNumber;              ///< run number
+    TString fRunTitle;               ///< run title
+    TString fSetup;                  ///< description of the setup of this run
+    TString fStartTime;              ///< start time of the run
+    TString fStartDate;              ///< start date of the run
+    time_t fStartDateTimeSec;        ///< start run given as time_t object
+    TString fStopTime;               ///< stop time of the run
+    TString fStopDate;               ///< stop date of the run
+    time_t fStopDateTimeSec;         ///< stop run given as time_t object
+    TString fCryo;                   ///< name of the cryo
+    TString fSample;                 ///< description of the sample
+    TString fOrientation;            ///< description of the orientation
+    TString fMagnet;                 ///< name of the sample magnet
+    Double_t fField;                 ///< magnetic field value in (G)
    PDoublePairVector fTemp;         ///< measured temperatures and standard deviations during the run
-    Double_t fEnergy{PMUSR_UNDEFINED};      ///< implantation energy of the muon
-    Double_t fTransport{PMUSR_UNDEFINED};   ///< LEM transport settings (Moderator HV)
+    Double_t fEnergy;                ///< implantation energy of the muon
+    Double_t fTransport;             ///< LEM transport settings (Moderator HV)
    PDoubleVector fRingAnode;        ///< LEM ring anode HVs (L,R[,T,B])
-    Double_t fTimeResolution{PMUSR_UNDEFINED}; ///< time resolution of the run in (ns)
+    Double_t fTimeResolution;        ///< 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.
 };
@@ -1057,7 +1050,6 @@ 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);
@@ -1071,7 +1063,6 @@ 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.
@@ -1088,7 +1079,6 @@ 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'
 };

 //-------------------------------------------------------------
@@ -1154,7 +1144,6 @@ 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]; }
@@ -1188,7 +1177,6 @@ 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; }
@@ -1222,7 +1210,6 @@ 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)

--- a/src/include/PRunDataHandler.h
+++ b/src/include/PRunDataHandler.h
@@ -30,10 +30,6 @@
 #ifndef _PRUNDATAHANDLER_H_
 #define _PRUNDATAHANDLER_H_

-#include <any>
-#include <iostream>
-#include <string>
-
 #include <TString.h>

 #include "PMusr.h"
@@ -436,8 +432,6 @@ 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();
@@ -449,7 +443,7 @@ 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 format, TString fln="");
+    virtual Bool_t WriteNexusFile(TString fln="");
    virtual Bool_t WriteWkmFile(TString fln="");
    virtual Bool_t WritePsiBinFile(TString fln="");
    virtual Bool_t WriteMudFile(TString fln="");
@@ -470,417 +464,4 @@ 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_
Author	SHA1	Message	Date
Andreas Suter	9d173203ff	fix git-revision.h generation: output to build tree and add missing dependencies All checks were successful Build and Deploy Documentation / build-and-deploy (push) Successful in 18s Details 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>	2026-01-29 19:52:16 +01:00
Andreas Suter	8b054b77b9	generate git-revision.h at build time instead of configure time All checks were successful Build and Deploy Documentation / build-and-deploy (push) Successful in 18s Details Replace execute_process with add_custom_target so the git revision check runs on every build, not just on cmake configure. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>	2026-01-29 19:35:20 +01:00
Andreas Suter	4e29ad6898	proper TDirectory handling for the histos. All checks were successful Build and Deploy Documentation / build-and-deploy (push) Successful in 19s Details	2026-01-26 20:32:34 +01:00
Andreas Suter	4ac7a7d01c	fixed missing TDirectory handling of RunSummary in dump_header.cpp All checks were successful Build and Deploy Documentation / build-and-deploy (push) Successful in 20s Details	2026-01-26 19:52:41 +01:00
Andreas Suter	227bfb7419	2nd spot for cmake version check for policy setting. All checks were successful Build and Deploy Documentation / build-and-deploy (push) Successful in 19s Details	2026-01-25 14:49:38 +01:00
Andreas Suter	70eb0397df	cmake version check for policy setting.	2026-01-25 14:45:46 +01:00
Andreas Suter	4de660788d	updated the copyright info. All checks were successful Build and Deploy Documentation / build-and-deploy (push) Successful in 26s Details	2026-01-25 07:42:29 +01:00
Andreas Suter	af3c8832fe	set cmake Boost find policy. All checks were successful Build and Deploy Documentation / build-and-deploy (push) Successful in 28s Details	2026-01-25 07:26:25 +01:00
Andreas Suter	123acec405	version update of the doxygen config file. All checks were successful Build and Deploy Documentation / build-and-deploy (push) Successful in 30s Details	2026-01-22 15:15:42 +01:00
Andreas Suter	eaa2ba8faf	further playing with the Prefs dialog. All checks were successful Build and Deploy Documentation / build-and-deploy (push) Successful in 18s Details	2026-01-21 12:19:34 +01:00
Andreas Suter	8b9ac6e5b1	further playing with the Prefs dialog. All checks were successful Build and Deploy Documentation / build-and-deploy (push) Successful in 26s Details	2026-01-21 12:16:27 +01:00
Andreas Suter	2601e80c8a	further playing with the Prefs dialog. All checks were successful Build and Deploy Documentation / build-and-deploy (push) Successful in 19s Details	2026-01-21 11:20:08 +01:00
Andreas Suter	1b91d8b281	increased size of prefs dialog, since it seems too small for the newest qt6 version, especially on macOS. All checks were successful Build and Deploy Documentation / build-and-deploy (push) Successful in 27s Details	2026-01-21 11:11:17 +01:00