Merge branch 'master' into feature/8221_schema_version refs #8221

Conflicts: Code/Mantid/instrument/BASIS_Definition.xml Code/Mantid/instrument/BASIS_Definition_0-20130719.xml Code/Mantid/instrument/NOMAD_Definition.xml Code/Mantid/instrument/POWGEN_Definition_2013-08-01.xml Code/Mantid/instrument/VISION_Definition.xml Code/Mantid/instrument/VISION_Definition_0-20131021.xml Code/Mantid/instrument/VISION_Definition_20131021-.xml
mantidproject · Oct 30, 2013 · 1685d25 · 1685d25
2 parents 26c216d + b5be1ab
commit 1685d25
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Showing 371 changed files with 53,743 additions and 24,648 deletions.
diff --git a/.gitattributes b/.gitattributes
@@ -8,6 +8,6 @@
 *.xml              hooks.MaxObjectKiB130902=2048
 
 # Allowing gSoap generated files to be committed.
-/Code/Mantid/Framework/ICat/inc/MantidICat/ICat3/GSoapGenerated/ICat3H.h              hooks.MaxObjectKiB130819=2048 
-/Code/Mantid/Framework/ICat/src/ICat3/GSoapGenerated/ICat3C.cpp                       hooks.MaxObjectKiB130819=5120
-/Code/Mantid/Framework/ICat/src/ICat4/GSoapGenerated/ICat4C.cpp                       hooks.MaxObjectKiB130819=2048
+/Code/Mantid/Framework/ICat/inc/MantidICat/ICat3/GSoapGenerated/ICat3H.h              hooks.MaxObjectKiB131025=2048 
+/Code/Mantid/Framework/ICat/src/ICat3/GSoapGenerated/ICat3C.cpp                       hooks.MaxObjectKiB131025=5120
+/Code/Mantid/Framework/ICat/src/ICat4/GSoapGenerated/ICat4C.cpp                       hooks.MaxObjectKiB131025=2048
diff --git a/Code/Mantid/CMakeLists.txt b/Code/Mantid/CMakeLists.txt
@@ -173,7 +173,11 @@ if ( ENABLE_CPACK )
     include ( CPackCommon )
 
     # Mac Packagemaker settings
-    set ( CPACK_RESOURCE_FILE_README ${CMAKE_SOURCE_DIR}/Installers/MacInstaller/MacOSX-README.rtf )
+    if (OSX_VERSION VERSION_LESS 10.8)
+      set ( CPACK_RESOURCE_FILE_README ${CMAKE_SOURCE_DIR}/Installers/MacInstaller/MacOSX-README.rtf )
+    else()
+      set ( CPACK_RESOURCE_FILE_README ${CMAKE_SOURCE_DIR}/Installers/MacInstaller/MacOSX10-8-README.rtf )
+    endif ()
     set ( CPACK_RESOURCE_FILE_LICENSE ${CMAKE_SOURCE_DIR}/Installers/WinInstaller/License.rtf )
 
     IF ( ${CMAKE_SYSTEM_NAME} STREQUAL "Linux" )

diff --git a/Code/Mantid/Framework/API/CMakeLists.txt b/Code/Mantid/Framework/API/CMakeLists.txt
@@ -297,6 +297,7 @@ set ( TEST_FILES
 	IEventListTest.h
 	IFunction1DTest.h
 	IFunctionMDTest.h
+	IkedaCarpenterModeratorTest.h
 	ILiveListenerTest.h
 	IMDWorkspaceTest.h
 	ISpectrumTest.h

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/Algorithm.h b/Code/Mantid/Framework/API/inc/MantidAPI/Algorithm.h
@@ -223,6 +223,12 @@ class MANTID_API_DLL Algorithm : public IAlgorithm, public Kernel::PropertyManag
   void setLogging(const bool value){g_log.setEnabled(value);}
   ///returns the status of logging, True = enabled
   bool isLogging() const {return g_log.getEnabled();}
+
+  ///sets the logging priority offset
+  void setLoggingOffset(const int value) {g_log.setLevelOffset(value);}
+  ///returns the logging priority offset
+  int getLoggingOffset() const {return g_log.getLevelOffset();}
+
   /// Returns a reference to the logger.
   Kernel::Logger& getLogger() const { return g_log; }
 

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/AlgorithmProxy.h b/Code/Mantid/Framework/API/inc/MantidAPI/AlgorithmProxy.h
@@ -124,6 +124,11 @@ namespace Mantid
       void setLogging(const bool value) { m_isLoggingEnabled=value; }
       /// Is the algorithm have logging enabled
       bool isLogging() const { return m_isLoggingEnabled; }
+
+      ///returns the logging priority offset
+      void setLoggingOffset(const int value)  { m_loggingOffset=value; }
+      ///returns the logging priority offset
+      int getLoggingOffset() const { return m_loggingOffset; }
 
       ///setting the child start progress
       void setChildStartProgress(const double startProgress)const;
@@ -166,6 +171,7 @@ namespace Mantid
       mutable boost::shared_ptr<Algorithm> m_alg;  ///< Shared pointer to a real algorithm. Created on demand
       bool m_isExecuted;     ///< Executed flag
       bool m_isLoggingEnabled;///< is the logging of the underlying algorithm enabled
+      int m_loggingOffset; ///< the logging priority offset
       bool m_rethrow; ///< Whether or not to rethrow exceptions.
       bool m_isChild; ///< Is this a child algo
 

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/IAlgorithm.h b/Code/Mantid/Framework/API/inc/MantidAPI/IAlgorithm.h
@@ -159,7 +159,11 @@ class MANTID_API_DLL IAlgorithm : virtual public Kernel::IPropertyManager
   ///Logging can be disabled by passing a value of false
   virtual void setLogging(const bool value) = 0;
   ///returns the status of logging, True = enabled
-  virtual bool isLogging() const = 0;
+  virtual bool isLogging() const = 0;  
+  ///gets the logging priority offset
+  virtual void setLoggingOffset(const int value) = 0;
+  ///returns the logging priority offset
+  virtual int getLoggingOffset() const = 0;
   ///setting the child start progress
   virtual void setChildStartProgress(const double startProgress)const = 0;
   /// setting the child end progress

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/IDomainCreator.h b/Code/Mantid/Framework/API/inc/MantidAPI/IDomainCreator.h
@@ -64,7 +64,7 @@ namespace Mantid
       virtual void initialize(Kernel::IPropertyManager* , const std::string&, DomainType) {}
 
       /// Toggle output of either just composite or composite + members
-      void separateCompositeMembersInOutput(const bool value);
+      void separateCompositeMembersInOutput(const bool value, const bool conv = false);
 
       /// Declare properties that specify the dataset within the workspace to fit to.
       /// @param suffix :: A suffix to give to all new properties.
@@ -117,6 +117,8 @@ namespace Mantid
       DomainType m_domainType;
       /// Output separate composite function values
       bool m_outputCompositeMembers;
+      /// Perform convolution of output composite components
+      bool m_convolutionCompositeMembers;
       /// Flag to ignore nans, infinities and zero errors.
       bool m_ignoreInvalidData;
     };

diff --git a/Code/Mantid/Framework/API/src/Algorithm.cpp b/Code/Mantid/Framework/API/src/Algorithm.cpp
@@ -951,6 +951,7 @@ namespace Mantid
       copyPropertiesFrom(proxy);
       m_algorithmID = proxy.getAlgorithmID();
       setLogging(proxy.isLogging());
+      setLoggingOffset(proxy.getLoggingOffset());
       setChild(proxy.isChild());
     }
 

diff --git a/Code/Mantid/Framework/API/src/AlgorithmProxy.cpp b/Code/Mantid/Framework/API/src/AlgorithmProxy.cpp
@@ -25,7 +25,7 @@ namespace Mantid
     PropertyManagerOwner(),_executeAsync(this,&AlgorithmProxy::executeAsyncImpl),
       m_name(alg->name()),m_category(alg->category()), m_categorySeparator(alg->categorySeparator()),
       m_alias(alg->alias()), m_version(alg->version()), m_alg(alg),
-      m_isExecuted(),m_isLoggingEnabled(true), m_rethrow(false),
+      m_isExecuted(),m_isLoggingEnabled(true), m_loggingOffset(0), m_rethrow(false),
       m_isChild(false)
     {
       if (!alg)

diff --git a/Code/Mantid/Framework/API/src/ExperimentInfo.cpp b/Code/Mantid/Framework/API/src/ExperimentInfo.cpp
@@ -963,6 +963,7 @@ namespace API
     }
     else
     {
+      if ( !instrumentFilename.empty() ) instrumentFilename = ConfigService::Instance().getInstrumentDirectory() + "/" + instrumentFilename;
       g_log.debug() << "Using instrument IDF XML text contained in nexus file.\n";
     }
 

diff --git a/Code/Mantid/Framework/API/src/IDomainCreator.cpp b/Code/Mantid/Framework/API/src/IDomainCreator.cpp
@@ -18,18 +18,25 @@ namespace API
   IDomainCreator::IDomainCreator( Kernel::IPropertyManager* manager,
     const std::vector<std::string>& workspacePropertyNames,
     DomainType domainType):
-  m_manager( manager ),
-  m_workspacePropertyNames( workspacePropertyNames ),
-    m_domainType( domainType ), m_outputCompositeMembers( false ), m_ignoreInvalidData( false )
+    m_manager( manager ),
+    m_workspacePropertyNames( workspacePropertyNames ),
+    m_domainType( domainType ),
+    m_outputCompositeMembers( false ),
+    m_convolutionCompositeMembers( false ),
+    m_ignoreInvalidData( false )
   {}
 
   /**
    * @param value If true then each composite is unrolled and its output is appended to
    * the default output, otherwise just the composite is used
+   * @param conv If true and the fitting function is Convolution and its model (function with
+   * index 1) is composite then output the components of the model convolved with the
+   * resolution (function index 0).
    */
-  void IDomainCreator::separateCompositeMembersInOutput(const bool value)
+  void IDomainCreator::separateCompositeMembersInOutput(const bool value, const bool conv)
   {
     m_outputCompositeMembers = value;
+    m_convolutionCompositeMembers = conv;
   }
 
   /**

diff --git a/Code/Mantid/Framework/API/src/IkedaCarpenterModerator.cpp b/Code/Mantid/Framework/API/src/IkedaCarpenterModerator.cpp
@@ -193,7 +193,7 @@ namespace Mantid
     }
 
     /**
-     * Return the value of time interpolated from the given time using the cached table
+     * Return the value of time interpolated from the given area using the cached table
      * @param area The value of the area to interpolate from
      * @return The time corresponding to this area linearly interpolated from the cached table
      */
@@ -212,7 +212,11 @@ namespace Mantid
       const unsigned int nsteps = (m_lookupSize - 1);
       const unsigned int indexBelow = static_cast<unsigned int>(std::floor(area*nsteps));
       const double step = area*nsteps - indexBelow;
-      return m_areaToTimeLookup[indexBelow]*(1.0 - step) + m_areaToTimeLookup[indexBelow + 1]*step;
+      if(indexBelow < nsteps )
+        return m_areaToTimeLookup[indexBelow]*(1.0 - step) + m_areaToTimeLookup[indexBelow + 1]*step;
+      else
+        return m_areaToTimeLookup[indexBelow]; // last edge value
+
     }
 
 
@@ -460,12 +464,12 @@ namespace Mantid
       {
         if(m_tau_f != 0.0)
         {
-          static const double c3 = 1.6666666666666666667e-01, c4 =-1.2500000000000000000e-01,
-                              c5 = 5.0000000000000000000e-02, c6 =-1.3888888888888888889e-02,
-                              c7 = 2.9761904761904761905e-03, c8 =-5.2083333333333333333e-04,
-                              c9 = 7.7160493827160493827e-05, c10 =-9.9206349206349206349e-06,
-                              c11= 1.1273448773448773449e-06, c12 =-1.1482216343327454439e-07,
-                              c13 = 1.0598968932302265636e-08;
+          const double c3 = 1.6666666666666666667e-01, c4 =-1.2500000000000000000e-01,
+                       c5 = 5.0000000000000000000e-02, c6 =-1.3888888888888888889e-02,
+                       c7 = 2.9761904761904761905e-03, c8 =-5.2083333333333333333e-04,
+                       c9 = 7.7160493827160493827e-05, c10 =-9.9206349206349206349e-06,
+                       c11= 1.1273448773448773449e-06, c12 =-1.1482216343327454439e-07,
+                       c13 = 1.0598968932302265636e-08;
 
           const double ax=x/m_tau_f;
           double funAx;