Refs #4024: going back to old Nexus (again!)

This reverts commit 34d300f.
mantidproject · Nov 22, 2011 · 5f2e4cc · 5f2e4cc
1 parent 34d300f
commit 5f2e4cc
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Showing 69 changed files with 3,343 additions and 398 deletions.
diff --git a/Code/Mantid/Build/CMake/CommonVatesSetup.cmake b/Code/Mantid/Build/CMake/CommonVatesSetup.cmake
@@ -14,6 +14,7 @@ Framework/DataHandling
 Framework/MDEvents
 Framework/MDAlgorithms
 Framework/Nexus
+Framework/NexusCPP
 )
 
 set ( COMMONVATES_SETUP_DONE TRUE )
diff --git a/Code/Mantid/CMakeLists.txt b/Code/Mantid/CMakeLists.txt
@@ -48,7 +48,8 @@ add_subdirectory ( Framework )
 include_directories ( Framework/Kernel/inc )
 include_directories ( Framework/Geometry/inc )
 include_directories ( Framework/API/inc )
-set ( CORE_MANTIDLIBS Kernel Geometry API ${NEXUS_LIBRARIES})
+include_directories ( Framework/NexusCPP/inc )
+set ( CORE_MANTIDLIBS Kernel Geometry API )
 
 add_subdirectory ( MantidQt )
 

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/BoxController.h b/Code/Mantid/Framework/API/inc/MantidAPI/BoxController.h
@@ -5,7 +5,7 @@
 #include "MantidKernel/MultiThreaded.h"
 #include "MantidKernel/System.h"
 #include "MantidKernel/ThreadPool.h"
-#include "nexus/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusFile.hpp"
 #include <boost/shared_ptr.hpp>
 #include <vector>
 

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/MatrixWorkspace.h b/Code/Mantid/Framework/API/inc/MantidAPI/MatrixWorkspace.h
@@ -23,7 +23,7 @@
 #include <set>
 #include "MantidAPI/ISpectrum.h"
 #include "MantidKernel/DateAndTime.h"
-#include "nexus/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusFile.hpp"
 
 namespace Mantid
 {

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/PropertyNexus.h b/Code/Mantid/Framework/API/inc/MantidAPI/PropertyNexus.h
@@ -3,7 +3,7 @@
 
 #include "MantidKernel/System.h"
 #include "MantidKernel/Property.h"
-#include "nexus/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusFile.hpp"
 
 
 namespace Mantid

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/Run.h b/Code/Mantid/Framework/API/inc/MantidAPI/Run.h
@@ -7,7 +7,7 @@
 #include "MantidKernel/TimeSplitter.h"
 #include <vector>
 #include "MantidKernel/Matrix.h"
-#include "nexus/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusFile.hpp"
 
 
 namespace Mantid

diff --git a/Code/Mantid/Framework/API/src/MatrixWorkspace.cpp b/Code/Mantid/Framework/API/src/MatrixWorkspace.cpp
@@ -20,7 +20,7 @@
 #include <numeric>
 #include "MantidAPI/NumericAxis.h"
 #include "MantidKernel/DateAndTime.h"
-#include "nexus/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusFile.hpp"
 
 using Mantid::Kernel::DateAndTime;
 using Mantid::Kernel::TimeSeriesProperty;

diff --git a/Code/Mantid/Framework/API/src/PropertyNexus.cpp b/Code/Mantid/Framework/API/src/PropertyNexus.cpp
@@ -1,7 +1,7 @@
 #include "MantidAPI/PropertyNexus.h"
 #include "MantidKernel/System.h"
-#include "nexus/NeXusException.hpp"
-#include "nexus/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusException.hpp"
+#include "MantidNexusCPP/NeXusFile.hpp"
 #include "MantidKernel/DateAndTime.h"
 #include "MantidKernel/TimeSeriesProperty.h"
 #include "MantidKernel/PropertyWithValue.h"
@@ -164,11 +164,7 @@ namespace PropertyNexus
   template <typename NumT>
   void savePropertyWithValue(::NeXus::File * file, PropertyWithValue<NumT> * prop)
   {
-    // Spaces are unacceptable in names - remove them
-    std::string name(prop->name());
-    for (size_t i=0; i<name.size(); i++)
-      if (name[i] == ' ') name[i] = '_';
-    file->makeGroup(name, "NXlog", 1);
+    file->makeGroup(prop->name(), "NXlog", 1);
     file->writeData("value", (*prop)() );
     file->closeGroup();
   }
@@ -177,11 +173,7 @@ namespace PropertyNexus
   /** Helper function to save a PropertyWithValue<> */
   void savePropertyWithValueString(::NeXus::File * file, PropertyWithValue<std::string> * prop)
   {
-    // Spaces are unacceptable in names - remove them
-    std::string name(prop->name());
-    for (size_t i=0; i<name.size(); i++)
-      if (name[i] == ' ') name[i] = '_';
-    file->makeGroup(name, "NXlog", 1);
+    file->makeGroup(prop->name(), "NXlog", 1);
     file->writeData("value", prop->value() );
     file->closeGroup();
   }
@@ -210,11 +202,7 @@ namespace PropertyNexus
   {
     std::vector<NumT> value = prop->valuesAsVector();
     if( value.empty() ) return;
-    // Spaces are unacceptable in names - remove them
-    std::string name(prop->name());
-    for (size_t i=0; i<name.size(); i++)
-      if (name[i] == ' ') name[i] = '_';
-    file->makeGroup(name, "NXlog", 1);
+    file->makeGroup(prop->name(), "NXlog", 1);
     file->writeData("value", value );
     saveTimeVector(file, prop);
     file->closeGroup();
@@ -226,12 +214,7 @@ namespace PropertyNexus
   {
     std::vector<std::string> values = prop->valuesAsVector();
     if( values.empty() ) return;
-
-    // Spaces are unacceptable in names - remove them
-    std::string name(prop->name());
-    for (size_t i=0; i<name.size(); i++)
-      if (name[i] == ' ') name[i] = '_';
-    file->makeGroup(name, "NXlog", 1);
+    file->makeGroup(prop->name(), "NXlog", 1);
 
     // Find the max length of any string
     size_t maxlen=0;

diff --git a/Code/Mantid/Framework/API/src/Sample.cpp b/Code/Mantid/Framework/API/src/Sample.cpp
@@ -7,7 +7,7 @@
 #include "MantidGeometry/IComponent.h"
 #include "MantidGeometry/Crystal/OrientedLattice.h"
 #include "MantidGeometry/Objects/ShapeFactory.h"
-#include "nexus/NeXusException.hpp"
+#include "MantidNexusCPP/NeXusException.hpp"
 
 using namespace Mantid::Kernel;
 using Mantid::Geometry::ShapeFactory;

diff --git a/Code/Mantid/Framework/CMakeLists.txt b/Code/Mantid/Framework/CMakeLists.txt
@@ -90,7 +90,9 @@ set ( MANTIDLIBS  ${Boost_LIBRARIES} ${POCO_LIBRARIES} ${TCMALLOC_LIBRARY} ${MPI
 add_custom_target ( FrameworkTests ) # target for all framework tests
 add_dependencies ( check FrameworkTests )
 
-set ( MANTIDLIBS ${MANTIDLIBS} ${NEXUS_LIBRARIES} )
+include_directories (NexusCPP/inc)
+add_subdirectory (NexusCPP)
+set ( MANTIDLIBS ${MANTIDLIBS} NexusCPP )
 
 include_directories (Kernel/inc)
 add_subdirectory (Kernel)
@@ -151,9 +153,8 @@ add_subdirectory (MDEvents)
 ###########################################################################
 
 set ( FRAMEWORK_LIBS Kernel Geometry API PythonAPI PythonKernelModule PythonAPIModule DataObjects
-                     DataHandling Nexus Algorithms CurveFitting ICat
-                     Crystal MDAlgorithms MDEvents WorkflowAlgorithms 
-                     Crystal MDAlgorithms MDEvents WorkflowAlgorithms 
+                     DataHandling Nexus NexusCPP Algorithms CurveFitting ICat
+                     Crystal MDAlgorithms MDEvents WorkflowAlgorithms
 )
 
 add_custom_target( Framework DEPENDS ${FRAMEWORK_LIBS} ) 

diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadEventNexus.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadEventNexus.h
@@ -7,8 +7,9 @@
 #include "MantidAPI/IDataFileChecker.h"
 #include "MantidDataObjects/EventWorkspace.h"
 
-#include "nexus/NeXusFile.hpp"
-#include "nexus/NeXusException.hpp"
+//Copy of the NexusCpp API was placed in MantidNexus
+#include "MantidNexusCPP/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusException.hpp"
 #include "MantidDataObjects/Events.h"
 
 

diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadLogsFromSNSNexus.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadLogsFromSNSNexus.h
@@ -9,8 +9,11 @@
 #include "MantidAPI/MatrixWorkspace.h"
 #include "MantidAPI/Sample.h"
 #include "MantidDataObjects/Workspace2D.h"
-#include "nexus/NeXusFile.hpp"
-#include "nexus/NeXusException.hpp"
+
+//Copy of the NexusCpp API was placed in MantidNexus
+#include "MantidNexusCPP/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusException.hpp"
+
 #include "MantidAPI/DeprecatedAlgorithm.h"
 
 namespace Mantid

diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadNexusLogs.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadNexusLogs.h
@@ -5,7 +5,7 @@
 // Includes
 //----------------------------------------------------------------------
 #include "MantidAPI/Algorithm.h"
-#include "nexus/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusFile.hpp"
 
 namespace Mantid
 {

diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadNexusMonitors.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadNexusMonitors.h
@@ -4,8 +4,9 @@
 #include "MantidAPI/Algorithm.h"
 #include "MantidAPI/MatrixWorkspace.h"
 #include <boost/scoped_array.hpp>
-#include "nexus/NeXusFile.hpp"
-#include "nexus/NeXusException.hpp"
+//Copy of the NexusCpp API was placed in MantidNexus
+#include "MantidNexusCPP/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusException.hpp"
 
 namespace Mantid
 {

diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadNexusProcessed.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadNexusProcessed.h
@@ -8,7 +8,7 @@
 #include "MantidAPI/IDataFileChecker.h"
 
 #include "MantidNexus/NexusClasses.h"
-#include "nexus/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusFile.hpp"
 
 namespace Mantid
 {

diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/PrecompiledHeader.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/PrecompiledHeader.h
@@ -2,7 +2,7 @@
 #define MANTID_DATAHANDLING_PRECOMPILEDHEADER_H_
 
 #include "MantidAPI/Algorithm.h"
-#include "nexus/NeXusFile.hpp"
-#include "nexus/NeXusException.hpp"
+#include "MantidNexusCPP/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusException.hpp"
 
 #endif // MANTID_DATAHANDLING_PRECOMPILEDHEADER_H_
diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXSPE.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXSPE.h
@@ -10,8 +10,10 @@
 #include "MantidAPI/Sample.h"
 #include "MantidDataObjects/Workspace2D.h"
 #include "MantidDataObjects/EventWorkspace.h"
-#include "nexus/NeXusFile.hpp"
-#include "nexus/NeXusException.hpp"
+
+//Copy of the NexusCpp API was placed in MantidNexus
+#include "MantidNexusCPP/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusException.hpp"
 
 namespace Mantid
 {

diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNexusProcessed.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNexusProcessed.h
@@ -62,7 +62,7 @@ namespace Mantid
       /// Algorithm's category for identification overriding a virtual method
       virtual const std::string category() const { return "DataHandling";}
 
-    protected:
+    private:
       /// Sets documentation strings for this algorithm
       virtual void initDocs();
       /// Overwrites Algorithm method.

diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveToSNSHistogramNexus.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveToSNSHistogramNexus.h
@@ -12,8 +12,10 @@
 #include "MantidDataObjects/Workspace2D.h"
 #include "MantidDataObjects/EventWorkspace.h"
 #include "MantidGeometry/Instrument/RectangularDetector.h"
-#include "nexus/NeXusFile.hpp"
-#include "nexus/NeXusException.hpp"
+
+//Copy of the NexusCpp API was placed in MantidNexus
+#include "MantidNexusCPP/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusException.hpp"
 
 using namespace ::NeXus;
 

diff --git a/Code/Mantid/Framework/DataHandling/src/LoadISISNexus2.cpp b/Code/Mantid/Framework/DataHandling/src/LoadISISNexus2.cpp
@@ -12,8 +12,8 @@
 #include "MantidGeometry/Instrument/XMLlogfile.h"
 #include "MantidGeometry/Instrument/Detector.h"
 
-#include "nexus/NeXusFile.hpp"
-#include "nexus/NeXusException.hpp"
+#include "MantidNexusCPP/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusException.hpp"
 
 #include "MantidAPI/LoadAlgorithmFactory.h"
 #include <Poco/Path.h>

diff --git a/Code/Mantid/Framework/DataHandling/src/LoadMuonNexus.cpp b/Code/Mantid/Framework/DataHandling/src/LoadMuonNexus.cpp
@@ -60,8 +60,8 @@ The subalgorithms used by LoadMuonNexus are:
 #include <boost/shared_ptr.hpp>
 #include "MantidNexus/MuonNexusReader.h"
 #include "MantidNexus/NexusClasses.h"
-#include "nexus/NeXusFile.hpp"
-#include "nexus/NeXusException.hpp"
+#include "MantidNexusCPP/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusException.hpp"
 
 namespace Mantid
 {

diff --git a/Code/Mantid/Framework/DataHandling/src/LoadMuonNexus2.cpp b/Code/Mantid/Framework/DataHandling/src/LoadMuonNexus2.cpp
@@ -12,8 +12,8 @@
 #include "MantidAPI/Progress.h"
 #include "MantidAPI/SpectraDetectorMap.h"
 #include "MantidNexus/NexusClasses.h"
-#include "nexus/NeXusFile.hpp"
-#include "nexus/NeXusException.hpp"
+#include "MantidNexusCPP/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusException.hpp"
 
 
 #include "MantidAPI/LoadAlgorithmFactory.h"

diff --git a/Code/Mantid/Framework/DataHandling/src/LoadNXSPE.cpp b/Code/Mantid/Framework/DataHandling/src/LoadNXSPE.cpp
@@ -8,8 +8,10 @@ Algorithm to load an NXSPE file into a workspace2D. It will create a new instrum
 #include "MantidKernel/UnitFactory.h"
 #include "MantidAPI/FileProperty.h"
 #include "MantidAPI/LoadAlgorithmFactory.h"
-#include "nexus/NeXusFile.hpp"
-#include "nexus/NeXusException.hpp"
+
+//Copy of the NexusCpp API was placed in MantidNexus
+#include "MantidNexusCPP/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusException.hpp"
 #include "MantidNexus/NexusClasses.h"
 #include <vector>
 #include <map>

diff --git a/Code/Mantid/Framework/DataHandling/src/LoadNexusLogs.cpp b/Code/Mantid/Framework/DataHandling/src/LoadNexusLogs.cpp
@@ -12,7 +12,7 @@ If you use [[LoadSNSEventNexus]] or [[LoadISISNexus]], calling this algorithm is
 // Includes
 //----------------------------------------------------------------------
 #include "MantidDataHandling/LoadNexusLogs.h"
-#include "nexus/NeXusException.hpp"
+#include "MantidNexusCPP/NeXusException.hpp"
 #include "MantidKernel/TimeSeriesProperty.h"
 #include "MantidKernel/LogParser.h"
 #include "MantidAPI/FileProperty.h"

diff --git a/Code/Mantid/Framework/DataHandling/src/LoadNexusProcessed.cpp b/Code/Mantid/Framework/DataHandling/src/LoadNexusProcessed.cpp
@@ -48,7 +48,7 @@ The subalgorithms used by LoadMuonNexus are:
 #include "MantidKernel/UnitFactory.h"
 #include "MantidNexus/NexusClasses.h"
 #include "MantidNexus/NexusFileIO.h"
-#include "nexus/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusFile.hpp"
 #include <boost/shared_ptr.hpp>
 #include <cmath>
 #include <Poco/DateTimeParser.h>

diff --git a/Code/Mantid/Framework/DataHandling/src/LoadTOFRawNexus.cpp b/Code/Mantid/Framework/DataHandling/src/LoadTOFRawNexus.cpp
@@ -12,7 +12,7 @@
 #include "MantidKernel/ArrayProperty.h"
 #include "MantidKernel/BoundedValidator.h"
 #include "MantidKernel/cow_ptr.h"
-#include "nexus/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusFile.hpp"
 #include <boost/algorithm/string/detail/classification.hpp>
 #include <boost/algorithm/string/split.hpp>
 
@@ -235,7 +235,7 @@ void LoadTOFRawNexus::countPixels(const std::string &nexusfilename, const std::s
 
           // Count how many pixels in the bank
           file->openData("pixel_id");
-          std::vector<int64_t> dims = file->getInfo().dims;
+          std::vector<int> dims = file->getInfo().dims;
           file->closeData();
 
           size_t newPixels = 1;
@@ -251,7 +251,7 @@ void LoadTOFRawNexus::countPixels(const std::string &nexusfilename, const std::s
         {
           // Get the size of the X vector
           file->openData(m_axisField);
-          std::vector<int64_t> dims = file->getInfo().dims;
+          std::vector<int> dims = file->getInfo().dims;
           // Find the units, if available
           if (file->hasAttr("units"))
             file->getAttr("units", m_xUnits);

diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXSPE.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXSPE.cpp
@@ -234,8 +234,8 @@ namespace Mantid
       nxFile.makeData("data", ::NeXus::FLOAT64, array_dims, false);
       nxFile.makeData("error", ::NeXus::FLOAT64, array_dims, false);
 
-      std::vector<int64_t> slab_start;
-      std::vector<int64_t> slab_size;
+      std::vector<int> slab_start;
+      std::vector<int> slab_size;
 
       // What size slabs are we going to write...
       slab_size.push_back(1);

diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNexusProcessed.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNexusProcessed.cpp
@@ -40,7 +40,7 @@ None
 #include "MantidKernel/ArrayProperty.h"
 #include "MantidKernel/ConfigService.h"
 #include "MantidNexus/NexusFileIO.h"
-#include "nexus/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusFile.hpp"
 #include <boost/shared_ptr.hpp>
 #include <cmath>
 #include <Poco/File.h>

diff --git a/Code/Mantid/Framework/DataHandling/src/UpdateInstrumentFromFile.cpp b/Code/Mantid/Framework/DataHandling/src/UpdateInstrumentFromFile.cpp
@@ -16,8 +16,8 @@ It is assumed that the positions specified in the raw file are all with respect
 #include "MantidAPI/MatrixWorkspace.h"
 #include "MantidAPI/SpectraDetectorMap.h"
 #include "LoadRaw/isisraw2.h"
-#include "nexus/NeXusFile.hpp"
-#include "nexus/NeXusException.hpp"
+#include "MantidNexusCPP/NeXusFile.hpp"
+#include "MantidNexusCPP/NeXusException.hpp"
 #include <boost/scoped_ptr.hpp>
 
 namespace Mantid