Merge branch 'master' into feature/10323_vesuvio_diffraction

Refs #10323

.gitignore

@@ -162,4 +162,8 @@ Desktop.ini
 # Mac OS X Finder
 .DS_Store
 
+# Ctags index files
+.tags
+.tags_sorted_by_file
+
 Code/Mantid/Vates/VatesSimpleGui/ViewWidgets/inc/MantidVatesSimpleGuiViewWidgets/LibHelper.h

Code/Mantid/Build/CMake/DarwinSetup.cmake

@@ -81,6 +81,14 @@ endif ()
 ###########################################################################
 set ( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -m64" )
 set ( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64 -std=c++0x" )
+set ( CMAKE_XCODE_ATTRIBUTE_CLANG_CXX_LANGUAGE_STANDARD "c++0x" )
+
+if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+  set ( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++" )
+  set ( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated-register" )
+  set ( CMAKE_XCODE_ATTRIBUTE_OTHER_CPLUSPLUSFLAGS "-Wno-deprecated-register")
+  set ( CMAKE_XCODE_ATTRIBUTE_CLANG_CXX_LIBRARY "libc++" )
+endif()
 
 if( ${CMAKE_C_COMPILER} MATCHES "icc.*$" )
   set ( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -no-intel-extensions" )
@@ -113,8 +121,16 @@ if (OSX_VERSION VERSION_LESS 10.9)
  set ( SITEPACKAGES /Library/Python/${PY_VER}/site-packages )
 else()
  # Assume we are using homebrew for now
+ # set Deployment target to 10.8
+ set ( CMAKE_OSX_SYSROOT /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk )
+ set ( CMAKE_OSX_ARCHITECTURES x86_64 )
+ set ( CMAKE_OSX_DEPLOYMENT_TARGET 10.8 )
  set ( PYQT4_PYTHONPATH /usr/local/lib/python${PY_VER}/site-packages/PyQt4 )
  set ( SITEPACKAGES /usr/local/lib/python${PY_VER}/site-packages )
+ # use homebrew OpenSSL package
+ EXEC_PROGRAM( brew ARGS info openssl | grep openssl: | cut -c 17-22 OUTPUT_VARIABLE _openssl_version )
+ MESSAGE(STATUS "OpenSSL version: ${_openssl_version}")
+ set ( OPENSSL_ROOT_DIR /usr/local/Cellar/openssl/${_openssl_version}/ )
 endif()
 
 # Python packages

Code/Mantid/Build/CMake/GNUSetup.cmake

@@ -6,16 +6,12 @@
 # project settings should be included in the relevant CMakeLists.txt file
 # for that project.
 
-# Get the GCC version
-EXEC_PROGRAM(${CMAKE_CXX_COMPILER} ARGS --version | cut -d \" \" -f 3 OUTPUT_VARIABLE _compiler_output)
-STRING(REGEX REPLACE ".*([0-9]\\.[0-9]\\.[0-9]).*" "\\1" GCC_COMPILER_VERSION ${_compiler_output})
-MESSAGE(STATUS "gcc version: ${GCC_COMPILER_VERSION}")
-
-# Export the GCC compiler version globally
-set(GCC_COMPILER_VERSION ${GCC_COMPILER_VERSION} CACHE INTERNAL "")
+# Set our own compiler version flag from the cmake one and export it globally
+set( GCC_COMPILER_VERSION ${CMAKE_CXX_COMPILER_VERSION} CACHE INTERNAL "")
+message( STATUS "gcc version: ${GCC_COMPILER_VERSION}" )
 
 # Global warning flags.
-set( GNUFLAGS "-Wall -Wextra -Wconversion -Winit-self -Wpointer-arith -Wcast-qual -Wcast-align -fno-common" ) 
+set( GNUFLAGS "-Wall -Wextra -Wconversion -Winit-self -Wpointer-arith -Wcast-qual -Wcast-align -fno-common" )
 # Disable some warnings about deprecated headers and type conversions that
 # we can't do anything about
 # -Wno-deprecated: Do not warn about use of deprecated headers.
@@ -38,4 +34,3 @@ set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${GNUFLAGS}" )
 set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${GNUFLAGS} -Woverloaded-virtual -fno-operator-names -std=c++0x" )
 # Cleanup
 set ( GNUFLAGS )
-

Code/Mantid/Framework/API/inc/MantidAPI/Algorithm.h

@@ -338,6 +338,11 @@ class MANTID_API_DLL Algorithm : public IAlgorithm, public Kernel::PropertyManag
   /// Pointer to the parent history object (if set)
   boost::shared_ptr<AlgorithmHistory> m_parentHistory;
 
+  /// One vector of workspaces for each input workspace property
+  std::vector<WorkspaceVector> m_groups;
+  /// Size of the group(s) being processed
+  size_t m_groupSize;
+
 private:
   /// Private Copy constructor: NO COPY ALLOWED
   Algorithm(const Algorithm&);
@@ -354,6 +359,9 @@ class MANTID_API_DLL Algorithm : public IAlgorithm, public Kernel::PropertyManag
 
   bool executeAsyncImpl(const Poco::Void & i);
 
+  // Report that the algorithm has completed.
+  void reportCompleted(const double& duration, const bool groupProcessing = false);
+
   // --------------------- Private Members -----------------------------------
   /// Poco::ActiveMethod used to implement asynchronous execution.
   Poco::ActiveMethod<bool, Poco::Void, Algorithm, Poco::ActiveStarter<Algorithm>> *m_executeAsync;
@@ -387,14 +395,10 @@ class MANTID_API_DLL Algorithm : public IAlgorithm, public Kernel::PropertyManag
   /// All the WorkspaceProperties that are Output (not inOut). Set in execute()
   std::vector<IWorkspaceProperty *> m_pureOutputWorkspaceProps;
 
-  /// One vector of workspaces for each input workspace property
-  std::vector<WorkspaceVector> m_groups;
   /// Pointer to the WorkspaceGroup (if any) for each input workspace property
   std::vector<boost::shared_ptr<WorkspaceGroup> > m_groupWorkspaces;
   /// If only one input is a group, this is its index. -1 if they are all groups
   int m_singleGroup;
-  /// Size of the group(s) being processed
-  size_t m_groupSize;
   /// All the groups have similar names (group_1, group_2 etc.)
   bool m_groupsHaveSimilarNames;
   /// A non-recursive mutex for thread-safety

Code/Mantid/Framework/API/inc/MantidAPI/IMDNode.h

@@ -71,6 +71,7 @@ class IMDNode
     *@param loadFileData -- if true, the data on HDD and not yet in memory are loaded into memory before deleting fileBacked information, 
                             if false, all on HDD contents are discarded, which can break the data integrity (used by destructor)  */
     virtual void clearFileBacked(bool loadFileData)=0;
+    virtual void reserveMemoryForLoad(uint64_t)=0;
 
     /**Save the box at specific disk position using the class, respoinsible for the file IO. */
     virtual void saveAt(API::IBoxControllerIO *const /*saver */,  uint64_t /*position*/)const=0;

Code/Mantid/Framework/API/inc/MantidAPI/ParamFunction.h

@@ -10,12 +10,6 @@
 #include <string>
 #include <vector>
 
-#ifndef HAS_UNORDERED_MAP_H
-#include <map>
-#else
-#include <tr1/unordered_map>
-#endif
-
 namespace Mantid
 {
 namespace API

Code/Mantid/Framework/API/inc/MantidAPI/Sample.h

@@ -5,9 +5,8 @@
 // Includes
 //------------------------------------------------------------------------------
 #include "MantidAPI/DllConfig.h"
-#include "MantidKernel/V3D.h"
-#include "MantidKernel/Material.h"
 #include "MantidGeometry/Objects/Object.h"
+#include "MantidKernel/V3D.h"
 #include <vector>
 
 
@@ -28,28 +27,28 @@ namespace Mantid
     //------------------------------------------------------------------------------
     class SampleEnvironment;
 
-    /** 
-      This class stores information about the sample used in particular 
+    /**
+      This class stores information about the sample used in particular
       run. It is a type of ObjComponent meaning it has a shape, a position
       and a material.
 
       Copyright &copy; 2007-2012 ISIS Rutherford Appleton Laboratory & NScD Oak Ridge National Laboratory
-      
+
       This file is part of Mantid.
-      
+
       Mantid 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 3 of the License, or
       (at your option) any later version.
-      
+
       Mantid 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, see <http://www.gnu.org/licenses/>.
-      
+
       File change history is stored at: <https://github.com/mantidproject/mantid>.
       Code Documentation is available at: <http://doxygen.mantidproject.org>
     */
@@ -82,10 +81,8 @@ namespace Mantid
 
       /** @name Material properties.*/
       //@{
-      /// Return the material
+      /// Return the material (convenience method)
       const Kernel::Material & getMaterial() const;
-      /// Set the type of material that this sample is composed from
-      void setMaterial(const Kernel::Material& material);
       //@}
 
       /** @name Access the environment information */
@@ -102,7 +99,7 @@ namespace Mantid
       const Geometry::OrientedLattice & getOrientedLattice() const;
       /// Get a reference to the sample's OrientedLattice
       Geometry::OrientedLattice & getOrientedLattice();
-      /** Set the pointer to OrientedLattice defining the sample's lattice and orientation. 
+      /** Set the pointer to OrientedLattice defining the sample's lattice and orientation.
           No copying is done in the class, but the class deletes pointer on destruction so the application, providing the pointer should not do it*/
       void setOrientedLattice(Geometry::OrientedLattice * latt);
       bool hasOrientedLattice() const;
@@ -129,18 +126,16 @@ namespace Mantid
       /// Sets the width
       void setWidth(double width);
       /// Returns the width
-      double getWidth() const;  
+      double getWidth() const;
       //@}
       /// Delete the oriented lattice
       void clearOrientedLattice();
 
-    private: 
+    private:
       /// The sample name
       std::string m_name;
       /// The sample shape object
       Geometry::Object m_shape;
-      /// The sample composition
-      Kernel::Material m_material;
       /// An owned pointer to the SampleEnvironment object
       boost::shared_ptr<SampleEnvironment> m_environment;
       /// Pointer to the OrientedLattice of the sample, NULL if not set.

Code/Mantid/Framework/API/inc/MantidAPI/SampleEnvironment.h

@@ -5,67 +5,69 @@
 // Includes
 //------------------------------------------------------------------------------
 #include "MantidAPI/DllConfig.h"
-#include "MantidGeometry/Instrument/CompAssembly.h"
+#include "MantidGeometry/Objects/Object.h"
+#include "MantidKernel/ClassMacros.h"
 
 namespace Mantid
 {
+  namespace Geometry
+  {
+    class Track;
+  }
   namespace API
   {
-    /** 
+    /**
       This class stores details regarding the sample environment that was used during
-      a specific run. It is implemented as a type of CompAssembly so that enviroment kits
-      consisting of objects made from different materials can be constructed easily.
-        
-      @author Martyn Gigg, Tessella plc
-      @date 23/11/2010
-      
+      a specific run. It is implemented as a collection of pairs of Object elements
+
       Copyright © 2007-2010 ISIS Rutherford Appleton Laboratory & NScD Oak Ridge National Laboratory
-      
+
       This file is part of Mantid.
-      
+
       Mantid 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 3 of the License, or
       (at your option) any later version.
-      
+
       Mantid 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, see <http://www.gnu.org/licenses/>.
-      
+
       File change history is stored at: <https://github.com/mantidproject/mantid>.
       Code Documentation is available at: <http://doxygen.mantidproject.org>
     */
-    class MANTID_API_DLL SampleEnvironment : public Geometry::CompAssembly
+    class MANTID_API_DLL SampleEnvironment
     {
     public:
       /// Constructor defining the name of the environment
       SampleEnvironment(const std::string & name);
-      /// Copy constructor
-      SampleEnvironment(const SampleEnvironment& original);
-      /// Clone the assembly
-      virtual Geometry::IComponent* clone() const;
-      /// Type of object
-      virtual std::string type() const {return "SampleEnvironment"; }
 
-      /// Override the default add member to only add components with a defined
-      /// shape
-      int add(IComponent* comp);
+      /// @return The name of kit
+      inline const std::string name() const { return m_name; }
+      /// @return The number of elements the environment is composed of
+      inline size_t nelements() const { return m_elements.size(); }
+      /// Return the bounding box of all of the elements
+      Geometry::BoundingBox boundingBox() const;
+
+      /// Add an element
+      void add(const Geometry::Object & element);
+
       /// Is the point given a valid point within the environment
       bool isValid(const Kernel::V3D & point) const;
       /// Update the given track with intersections within the environment
       void interceptSurfaces(Geometry::Track & track) const;
 
     private:
-      /// Default constructor
-      SampleEnvironment();
-      /// Assignment operator
-      SampleEnvironment& operator=(const SampleEnvironment&);
-
+      DISABLE_DEFAULT_CONSTRUCT(SampleEnvironment)
 
+      // Name of the kit
+      std::string m_name;
+      // The elements
+      std::vector<Geometry::Object> m_elements;
     };
   }
 }