Merge branch 'master' of github.com:mantidproject/mantid

mantidproject · Nov 23, 2011 · 5ed21f7 · 5ed21f7
2 parents ef92049 + f95d505
commit 5ed21f7
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Showing 103 changed files with 3,830 additions and 604 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/ISpectrum.h b/Code/Mantid/Framework/API/inc/MantidAPI/ISpectrum.h
@@ -71,6 +71,9 @@ namespace API
     virtual const MantidVec& dataX() const;
     virtual const MantidVec& dataDx() const;
 
+    virtual const MantidVec& readX() const;
+    virtual const MantidVec& readDx() const;
+
     virtual MantidVecPtr ptrX() const;
 
     virtual void setData(const MantidVec& Y) = 0;
@@ -89,6 +92,8 @@ namespace API
 
     virtual const MantidVec& dataY() const = 0;
     virtual const MantidVec& dataE() const = 0;
+    virtual const MantidVec& readY() const;
+    virtual const MantidVec& readE() const;
 
     virtual size_t getMemorySize() const = 0;
 

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
 {
@@ -187,6 +187,10 @@ namespace Mantid
       /// Returns the error const
       virtual const MantidVec& dataDx(const std::size_t index) const { return getSpectrum(index)->dataDx(); }
 
+      virtual double getXMin() const;
+      virtual double getXMax() const;
+      virtual void getXMinMax(double &xmin, double &xmax) const;
+
       /// Returns a pointer to the x data
       virtual Kernel::cow_ptr<MantidVec> refX(const std::size_t index) const { return getSpectrum(index)->ptrX(); }
 

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/ISpectrum.cpp b/Code/Mantid/Framework/API/src/ISpectrum.cpp
@@ -104,6 +104,23 @@ namespace API
   const MantidVec& ISpectrum::dataDx() const
   { return *refDx; }
 
+
+  /// Returns the x data const
+  const MantidVec& ISpectrum::readX() const
+  { return *refX; }
+
+  /// Returns the x error data const
+  const MantidVec& ISpectrum::readDx() const
+  { return *refDx; }
+
+  /// Returns the y data const
+  const MantidVec& ISpectrum::readY() const
+  { return this->dataY(); }
+
+  /// Returns the y error data const
+  const MantidVec& ISpectrum::readE() const
+  { return this->dataE(); }
+
   /// Returns a pointer to the x data
   MantidVecPtr ISpectrum::ptrX() const
   { return refX; }

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;
@@ -652,6 +652,42 @@ namespace Mantid
       } // for each detector ID in the list
     }
 
+    double MatrixWorkspace::getXMin() const
+    {
+      double xmin;
+      double xmax;
+      this->getXMinMax(xmin, xmax); // delagate to the proper code
+      return xmin;
+    }
+
+    double MatrixWorkspace::getXMax() const
+    {
+      double xmin;
+      double xmax;
+      this->getXMinMax(xmin, xmax); // delagate to the proper code
+      return xmax;
+    }
+
+    void MatrixWorkspace::getXMinMax(double &xmin, double &xmax) const
+    {
+      // set to crazy values to start
+      xmin = std::numeric_limits<double>::max();
+      xmax = -1.0 * xmin;
+      size_t numberOfSpectra = this->getNumberHistograms();
+
+      // determine the data range
+      double temp;
+      for (size_t workspaceIndex = 0; workspaceIndex < numberOfSpectra; workspaceIndex++)
+      {
+        const MantidVec& dataX = this->readX(workspaceIndex); // force using const version
+        temp = dataX.front();
+        if (temp < xmin)
+          xmin = temp;
+        temp = dataX.back();
+        if (temp > xmax)
+          xmax = temp;
+      }
+    }
 
     //---------------------------------------------------------------------------------------
     /** Integrate all the spectra in the matrix workspace within the range given.

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/Algorithms/inc/MantidAlgorithms/DiffractionFocussing2.h b/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/DiffractionFocussing2.h
@@ -110,13 +110,13 @@ class DLLExport DiffractionFocussing2: public API::Algorithm
   int validateSpectrumInGroup(size_t wi);
 
   /// Shared pointer to a mutable input workspace
-  API::MatrixWorkspace_sptr matrixInputW;
+  API::MatrixWorkspace_sptr m_matrixInputW;
 
   /// Grouping workspace with groups to build
   Mantid::DataObjects::GroupingWorkspace_sptr groupWS;
 
   /// Shared pointer to the event workspace
-  DataObjects::EventWorkspace_sptr eventW;
+  DataObjects::EventWorkspace_sptr m_eventW;
 
 
   // This map does not need to be ordered, just a lookup for udet