Merge branch 'master' into feature/7253_workspace_groups_and_dock

Conflicts: Code/Mantid/Framework/WorkflowAlgorithms/src/AlignAndFocusPowder.cpp Re #7253
mantidproject · Jul 3, 2013 · fe478a4 · fe478a4
2 parents 889cf9f + 399f9b7
commit fe478a4
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diff --git a/Code/Mantid/Build/CMake/WindowsNSIS.cmake b/Code/Mantid/Build/CMake/WindowsNSIS.cmake
@@ -13,7 +13,7 @@
     set( CPACK_GENERATOR "NSIS" )
     set( CPACK_INSTALL_PREFIX "/")
     set( CPACK_NSIS_DISPLAY_NAME "Mantid${CPACK_PACKAGE_SUFFIX}")
-    set( CPACK_PACKAGE_NAME "Mantid${CPACK_PACKAGE_SUFFIX}" )
+    set( CPACK_PACKAGE_NAME "mantid${CPACK_PACKAGE_SUFFIX}" )
     set( CPACK_PACKAGE_INSTALL_DIRECTORY "MantidInstall${CPACK_PACKAGE_SUFFIX}") 
     set( CPACK_NSIS_INSTALL_ROOT "C:")
     set( CPACK_PACKAGE_EXECUTABLES "MantidPlot;MantidPlot")

diff --git a/Code/Mantid/Build/wiki_tools.py b/Code/Mantid/Build/wiki_tools.py
@@ -589,7 +589,7 @@ def do_make_wiki(algo_name, version, latest_version):
     """ 
 
     external_image = "http://download.mantidproject.org/algorithm_screenshots/ScreenShotImages/%s_dlg.png" % algo_name  
-    out = "<anchor url='%s'><img width=400px align='right' src='%s' style='position:relative; z-index:1000; padding-left:5px;'></anchor>\n\n" % (external_image, external_image)  
+    out = "<anchor url='%s'><img width=400px src='%s' style='position:relative; z-index:1000; padding-left:5px; float:right;'></anchor>\n\n" % (external_image, external_image)  
 
     # Deprecated algorithms: Simply return the deprecation message
     print "Creating... ", algo_name, version
@@ -623,6 +623,14 @@ def do_make_wiki(algo_name, version, latest_version):
         out += " " + create_function_signature(alg, algo_name) + "\n\n" 
     out += "<br clear=all>\n\n" 
     out += custom_usage
+
+    # If there is an alias put it in
+    alias = alg.alias().strip()
+    if len(alias) > 0:
+        out += ("== Alias ==\n\n")
+        out += "This algorithm is also called '%s'\n\n" % alias
+
+    # Table of properties
     out += "== Properties ==\n\n"
 
     out += """{| border="1" cellpadding="5" cellspacing="0" 

diff --git a/Code/Mantid/CMakeLists.txt b/Code/Mantid/CMakeLists.txt
@@ -104,13 +104,24 @@ add_subdirectory ( QtPropertyBrowser )
 # Flag that this is a full build, i.e not framework only
 set( FULL_PACKAGE_BUILD 1 )
 
+# Framework Build options
+set ( CXXTEST_SINGLE_LOGFILE CACHE BOOL "Switch to have the tests for each package run together")
+set ( CXXTEST_ADD_PERFORMANCE OFF CACHE BOOL "Switch to add Performance tests to the list of tests run by ctest?")
+set ( MAKE_REMOTE_JOBS ON CACHE BOOL "Add code for executing algorithms on a remote cluster")
+
 add_subdirectory ( Framework )
 
 include_directories ( Framework/Kernel/inc )
 include_directories ( Framework/Geometry/inc )
 include_directories ( Framework/API/inc )
+
 set ( CORE_MANTIDLIBS Kernel Geometry API )
 
+if ( MAKE_REMOTE_JOBS )
+  include_directories ( Framework/Remote/inc )
+  LIST( APPEND CORE_MANTIDLIBS Remote)
+endif (MAKE_REMOTE_JOBS)
+
 # Add a target for all GUI tests
 add_custom_target ( GUITests ) 
 add_dependencies ( check GUITests )
@@ -125,9 +136,8 @@ if ( UNIX )
   set ( UNITY_BUILD OFF CACHE BOOL "Switch for utilising unity builds. Faster builds for selected components.")
 endif ( UNIX )
 
+# VATES flag. Requires ParaView
 set ( MAKE_VATES OFF CACHE BOOL "Switch for compiling the Vates project")
-set ( CXXTEST_SINGLE_LOGFILE CACHE BOOL "Switch to have the tests for each package run together")
-set ( CXXTEST_ADD_PERFORMANCE OFF CACHE BOOL "Switch to add Performance tests to the list of tests run by ctest?") 
 
 if ( MAKE_VATES )
   add_subdirectory ( Vates )

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/CompositeFunction.h b/Code/Mantid/Framework/API/inc/MantidAPI/CompositeFunction.h
@@ -144,9 +144,6 @@ class MANTID_API_DLL CompositeFunction : public virtual IFunction
   /// Remove a constraint
   void removeConstraint(const std::string& parName);
 
-  /// Set a value to attribute attName
-  virtual void setAttribute(const std::string& attName,const Attribute& );
-
              /* CompositeFunction own methods */
 
   /// Add a function at the back of the internal function list
@@ -169,8 +166,6 @@ class MANTID_API_DLL CompositeFunction : public virtual IFunction
   std::string parameterLocalName(size_t i)const;
   /// Check the function.
   void checkFunction();
-  /// Enable/disable numeric derivative calculation
-  void useNumericDerivatives( bool yes ) const;
 
   /// Returns the number of attributes associated with the function
   virtual size_t nLocalAttributes()const {return 0;}
@@ -221,7 +216,6 @@ class MANTID_API_DLL CompositeFunction : public virtual IFunction
   /// Function counter to be used in nextConstraint
   mutable size_t m_iConstraintFunction;
   /// Flag set to use numerical derivatives
-  mutable bool m_useNumericDerivatives;
 };
 
 ///shared pointer to the composite function base class

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/IDomainCreator.h b/Code/Mantid/Framework/API/inc/MantidAPI/IDomainCreator.h
@@ -59,7 +59,7 @@ namespace Mantid
         const std::vector<std::string>& workspacePropertyNames,
         DomainType domainType = Simple);
       /// Virtual destructor
-      virtual ~IDomainCreator() {};
+      virtual ~IDomainCreator() {}
       /// Initialize
       virtual void initialize(Kernel::IPropertyManager* , const std::string&, DomainType) {}
 
@@ -103,6 +103,9 @@ namespace Mantid
       /// Return the size of the domain to be created.
       virtual size_t getDomainSize() const = 0;
 
+      /// Set to ignore invalid data
+      void ignoreInvalidData( bool yes ) {m_ignoreInvalidData = yes;}
+
     protected:
       /// Declare a property to the algorithm
       void declareProperty(Kernel::Property* prop,const std::string& doc);
@@ -114,6 +117,8 @@ namespace Mantid
       DomainType m_domainType;
       /// Output separate composite function values
       bool m_outputCompositeMembers;
+      /// Flag to ignore nans, infinities and zero errors.
+      bool m_ignoreInvalidData;
     };
 
     /// Typedef for a shared pointer to IDomainCreator.

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/IEventList.h b/Code/Mantid/Framework/API/inc/MantidAPI/IEventList.h
@@ -61,11 +61,19 @@ namespace API
     virtual void addPulsetime(const double seconds) = 0;
     /// Mask a given TOF range
     virtual void maskTof(const double tofMin, const double tofMax) = 0;
-    /// Return the list of TOF values
-    virtual void getTofs(std::vector<double>& tofs) const = 0;
-    /// Return the list of TOF values
+	/// Return the list of TOF values
     virtual std::vector<double> getTofs() const = 0;
     /// Return the list of TOF values
+    virtual void getTofs(std::vector<double>& tofs) const = 0;
+    /// Return the list of event weight  values
+    virtual std::vector<double> getWeights() const = 0;
+	/// Return the list of event weight values
+    virtual void getWeights(std::vector<double>& weights) const = 0;
+	/// Return the list of event weight error values
+    virtual std::vector<double> getWeightErrors() const = 0;
+	/// Return the list of event weight error values
+    virtual void getWeightErrors(std::vector<double>& weightErrors) const = 0;
+    /// Return the list of pulse time values
     virtual std::vector<Mantid::Kernel::DateAndTime> getPulseTimes() const = 0;
     /// Get the minimum TOF from the list
     virtual double getTofMin() const = 0;

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/IMDNode.h b/Code/Mantid/Framework/API/inc/MantidAPI/IMDNode.h
@@ -187,6 +187,10 @@ class IMDNode
     virtual  uint32_t getDepth() const=0;
     virtual signal_t getSignalNormalized() const=0;
 
+    virtual void calcVolume()=0;
+    virtual void setInverseVolume(const coord_t )=0;
+    virtual void setSignal(const signal_t )=0;
+    virtual void setErrorSquared(const signal_t )=0;
 
     // -------------------------------- Geometry/vertexes-Related -------------------------------------------
     virtual std::vector<Mantid::Kernel::VMD> getVertexes() const =0;

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/IPeakFunction.h b/Code/Mantid/Framework/API/inc/MantidAPI/IPeakFunction.h
@@ -64,6 +64,9 @@ class MANTID_API_DLL IPeakFunction : public IFunctionWithLocation
   static int s_peakRadius; 
 };
 
+typedef boost::shared_ptr<IPeakFunction> IPeakFunction_sptr;
+typedef boost::shared_ptr<const IPeakFunction> IPeakFunction_const_sptr;
+
 } // namespace API
 } // namespace Mantid
 

diff --git a/Code/Mantid/Framework/API/src/CompositeFunction.cpp b/Code/Mantid/Framework/API/src/CompositeFunction.cpp
@@ -55,8 +55,7 @@ DECLARE_FUNCTION(CompositeFunction)
 
 /// Default constructor
 CompositeFunction::CompositeFunction(): 
-m_nParams(0),
-m_useNumericDerivatives(false)
+m_nParams(0)
 {
   declareAttribute("NumDeriv", Attribute(false));
 }
@@ -185,7 +184,7 @@ void CompositeFunction::function(const FunctionDomain& domain, FunctionValues& v
  */
 void CompositeFunction::functionDeriv(const FunctionDomain& domain, Jacobian& jacobian)
 {
-  if ( m_useNumericDerivatives )
+  if ( getAttribute("NumDeriv").asBool() )
   {
     calNumericalDeriv(domain, jacobian);
   }
@@ -741,7 +740,7 @@ void CompositeFunction::setUpForFit()
 
   // instead of automatically switching to numeric derivatives
   // log a warning about a danger of not using it
-  if ( !m_useNumericDerivatives ) 
+  if ( !getAttribute("NumDeriv").asBool() )
   {
     for(size_t i = 0; i < nParams(); ++i)
     {
@@ -825,25 +824,5 @@ IFunction_sptr CompositeFunction::getContainingFunction(const ParameterReference
   return IFunction_sptr();
 }
 
-/**
- * Enable/disable numeric derivative calculation.
- * @param yes :: Set to true to use numeric derivative calculation.
- */
-void CompositeFunction::useNumericDerivatives( bool yes ) const
-{
-  m_useNumericDerivatives = yes;
-}
-
-/// Set a value to attribute attName
-void CompositeFunction::setAttribute(const std::string& attName,const Attribute& att)
-{
-  storeAttributeValue( attName, att );
-
-  if ( attName == "NumDeriv" )
-  {
-    useNumericDerivatives( att.asBool() );
-  }
-}
-
 } // namespace API
 } // namespace Mantid
diff --git a/Code/Mantid/Framework/API/src/IDomainCreator.cpp b/Code/Mantid/Framework/API/src/IDomainCreator.cpp
@@ -20,7 +20,7 @@ namespace API
     DomainType domainType):
   m_manager( manager ),
   m_workspacePropertyNames( workspacePropertyNames ),
-  m_domainType( domainType ), m_outputCompositeMembers(false)
+    m_domainType( domainType ), m_outputCompositeMembers( false ), m_ignoreInvalidData( false )
   {}
 
   /**

diff --git a/Code/Mantid/Framework/Algorithms/CMakeLists.txt b/Code/Mantid/Framework/Algorithms/CMakeLists.txt
@@ -20,7 +20,7 @@ set ( SRC_FILES
 	src/BinaryOperation.cpp
 	src/CalMuonDeadTime.cpp
 	src/CalculateEfficiency.cpp
-        src/CalculateFlatBackground.cpp
+	src/CalculateFlatBackground.cpp
 	src/CalculateTransmission.cpp
 	src/CalculateTransmissionBeamSpreader.cpp
 	src/CalculateZscore.cpp
@@ -34,6 +34,7 @@ set ( SRC_FILES
 	src/CloneWorkspace.cpp
 	src/CommutativeBinaryOperation.cpp
 	src/ConjoinWorkspaces.cpp
+	src/ConvertAxisByFormula.cpp
 	src/ConvertFromDistribution.cpp
 	src/ConvertMDHistoToMatrixWorkspace.cpp
 	src/ConvertSpectrumAxis.cpp
@@ -82,6 +83,7 @@ set ( SRC_FILES
 	src/ExportTimeSeriesLog.cpp
 	src/ExtractFFTSpectrum.cpp
 	src/ExtractMask.cpp
+	src/ExtractMaskToTable.cpp
 	src/ExtractMasking.cpp
 	src/ExtractSingleSpectrum.cpp
 	src/FFT.cpp
@@ -118,6 +120,7 @@ set ( SRC_FILES
 	src/He3TubeEfficiency.cpp
 	src/IQTransform.cpp
 	src/IdentifyNoisyDetectors.cpp
+	src/IntegrateByComponent.cpp
 	src/Integration.cpp
 	src/InterpolatingRebin.cpp
 	src/InvertMask.cpp
@@ -131,6 +134,7 @@ set ( SRC_FILES
 	src/MergeRuns.cpp
 	src/Min.cpp
 	src/Minus.cpp
+	src/ModeratorTzero.cpp
 	src/ModeratorTzeroLinear.cpp
 	src/MonteCarloAbsorption.cpp
 	src/MultipleScatteringCylinderAbsorption.cpp
@@ -170,6 +174,7 @@ set ( SRC_FILES
 	src/RemoveLowResTOF.cpp
 	src/RemovePromptPulse.cpp
 	src/RenameWorkspace.cpp
+        src/RenameWorkspaces.cpp
 	src/ReplaceSpecialValues.cpp
 	src/ResampleX.cpp
 	src/ResetNegatives.cpp
@@ -248,6 +253,7 @@ set ( INC_FILES
 	inc/MantidAlgorithms/CloneWorkspace.h
 	inc/MantidAlgorithms/CommutativeBinaryOperation.h
 	inc/MantidAlgorithms/ConjoinWorkspaces.h
+	inc/MantidAlgorithms/ConvertAxisByFormula.h
 	inc/MantidAlgorithms/ConvertFromDistribution.h
 	inc/MantidAlgorithms/ConvertMDHistoToMatrixWorkspace.h
 	inc/MantidAlgorithms/ConvertSpectrumAxis.h
@@ -296,6 +302,7 @@ set ( INC_FILES
 	inc/MantidAlgorithms/ExportTimeSeriesLog.h
 	inc/MantidAlgorithms/ExtractFFTSpectrum.h
 	inc/MantidAlgorithms/ExtractMask.h
+	inc/MantidAlgorithms/ExtractMaskToTable.h
 	inc/MantidAlgorithms/ExtractMasking.h
 	inc/MantidAlgorithms/ExtractSingleSpectrum.h
 	inc/MantidAlgorithms/FFT.h
@@ -333,6 +340,7 @@ set ( INC_FILES
 	inc/MantidAlgorithms/He3TubeEfficiency.h
 	inc/MantidAlgorithms/IQTransform.h
 	inc/MantidAlgorithms/IdentifyNoisyDetectors.h
+	inc/MantidAlgorithms/IntegrateByComponent.h
 	inc/MantidAlgorithms/Integration.h
 	inc/MantidAlgorithms/InterpolatingRebin.h
 	inc/MantidAlgorithms/InvertMask.h
@@ -346,6 +354,7 @@ set ( INC_FILES
 	inc/MantidAlgorithms/MergeRuns.h
 	inc/MantidAlgorithms/Min.h
 	inc/MantidAlgorithms/Minus.h
+	inc/MantidAlgorithms/ModeratorTzero.h
 	inc/MantidAlgorithms/ModeratorTzeroLinear.h
 	inc/MantidAlgorithms/MonteCarloAbsorption.h
 	inc/MantidAlgorithms/MultipleScatteringCylinderAbsorption.h
@@ -385,6 +394,7 @@ set ( INC_FILES
 	inc/MantidAlgorithms/RemoveLowResTOF.h
 	inc/MantidAlgorithms/RemovePromptPulse.h
 	inc/MantidAlgorithms/RenameWorkspace.h
+        inc/MantidAlgorithms/RenameWorkspaces.h
 	inc/MantidAlgorithms/ReplaceSpecialValues.h
 	inc/MantidAlgorithms/ResampleX.h
 	inc/MantidAlgorithms/ResetNegatives.h
@@ -474,6 +484,7 @@ set ( TEST_FILES
 	CommutativeBinaryOperationTest.h
 	CompressedRebinTest.h
 	ConjoinWorkspacesTest.h
+	ConvertAxisByFormulaTest.h
 	ConvertFromDistributionTest.h
 	ConvertSpectrumAxisTest.h
 	ConvertTableToMatrixWorkspaceTest.h
@@ -516,6 +527,7 @@ set ( TEST_FILES
 	ExportTimeSeriesLogTest.h
 	ExtractFFTSpectrumTest.h
 	ExtractMaskTest.h
+	ExtractMaskToTableTest.h
 	ExtractSingleSpectrumTest.h
 	FFTDerivativeTest.h
 	FFTSmooth2Test.h
@@ -547,6 +559,7 @@ set ( TEST_FILES
 	He3TubeEfficiencyTest.h
 	IQTransformTest.h
 	IdentifyNoisyDetectorsTest.h
+	IntegrateByComponentTest.h
 	IntegrationTest.h
 	InterpolatingRebinTest.h
 	InvertMaskTest.h
@@ -557,6 +570,7 @@ set ( TEST_FILES
 	MedianDetectorTestTest.h
 	MergeRunsTest.h
 	MinusTest.h
+	ModeratorTzeroTest.h
 	ModeratorTzeroLinearTest.h
 	MonteCarloAbsorptionTest.h
 	MultipleScatteringCylinderAbsorptionTest.h
@@ -592,6 +606,7 @@ set ( TEST_FILES
 	RemoveExpDecayTest.h
 	RemoveLowResTOFTest.h
 	RemovePromptPulseTest.h
+	RenameWorkspacesTest.h
 	RenameWorkspaceTest.h
 	ReplaceSpecialValuesTest.h
 	ResampleXTest.h