Merge branch 'master' into bugfix/8614_letReduction

Code/Mantid/Build/dev-packages/rpm/mantid-developer/mantid-developer-f20.spec

@@ -0,0 +1,105 @@
+Name:           mantid-developer
+Version:        1.3
+Release:        3%{?dist}
+Summary:        Meta Package to install dependencies for Mantid Development
+
+Group:          Development/Tools
+License:        GPL
+
+BuildRoot:      %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+
+Requires: rpmfusion-nonfree-release
+Requires: cmake-gui >= 2.8.5
+Requires: boost-devel
+Requires: gperftools-devel
+Requires: gperftools-libs
+Requires: gcc-c++
+Requires: git-all
+Requires: gsl-devel
+Requires: hdf-devel
+Requires: hdf5-devel
+Requires: muParser-devel
+Requires: mxml-devel
+Requires: nexus >= 4.2
+Requires: nexus-devel >= 4.2
+Requires: numpy
+Requires: OCE-devel
+Requires: poco-devel
+Requires: PyQt4-devel
+Requires: python-devel
+Requires: python-sphinx
+Requires: qscintilla-devel
+Requires: qt-devel >= 4.6
+Requires: qwt5-qt4-devel
+Requires: qwtplot3d-qt4-devel
+Requires: redhat-lsb
+Requires: rpmdevtools
+Requires: sip-devel
+Requires: git
+Requires: openssl-devel
+Requires: texlive-latex
+Requires: dvipng
+Requires: qt-devel
+Requires: qt-assistant
+
+BuildArch: noarch
+
+%description
+A virtual package which requires all the dependencies and tools that are 
+required for Mantid development.
+
+%prep
+
+%build
+
+%install
+
+%clean
+
+%post
+# Remove myself once I have installed all the required packages.
+#rpm -e %{name}
+
+%files
+
+%changelog
+* Fri Dec 20 2013 Stuart Campbell <campbellsi@ornl.gov>
+- Added python-sphinx
+
+* Thu Dec 19 2013 Stuart Campbell <campbellsi@ornl.gov>
+- Changed to use OCE rather than OpenCASCADE.
+
+* Tue Aug 20 2013 Peter Peterson <petersonpf@ornl.gov>
+- Removed things not necessary for fedora 19.
+
+* Tue May 07 2013 Stuart Campbell <campbellsi@ornl.gov>
+- Added dvipng and latex for qt-assistant stuff
+- Added software collection dependencies
+
+* Thu Jun  7 2012 Russell Taylor <taylorrj@ornl.gov>
+- Remove gmock & gtest now that we include them in our repo
+- Remove subversion dependency now that we use git
+
+* Mon Mar 19 2012 Stuart Campbell <campbellsi@ornl.gov>
+- Updated for google-perftools -> gperftools package rename.
+
+* Wed Feb 22 2012 Stuart Campbell <campbellsi@ornl.gov>
+- Added nexus as it is not required by it's devel package.
+
+* Wed Feb 22 2012 Stuart Campbell <campbellsi@ornl.gov>
+- Added git as a dependency
+- Added openssl-devel dependency
+
+* Mon Feb 20 2012 Stuart Campbell <campbellsi@ornl.gov>
+- Added dependency on NeXus development after nexus rpm split.
+- Updated CMake dependency to 2.8.5 following 'the virus'!
+- Added Google Mock and GTest.
+
+* Fri Jun  3 2011 Stuart Campbell <campbellsi@ornl.gov>
+- Added rpmdevtools and lsb dependencies
+
+* Fri Jun  3 2011 Stuart Campbell <campbellsi@ornl.gov>
+- Added versions for some packages
+
+* Fri Jun  3 2011 Stuart Campbell <campbellsi@ornl.gov>
+- Initial release

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

@@ -8,9 +8,11 @@
 #include "MantidAPI/DllConfig.h"
 #include "MantidKernel/DynamicFactory.h"
 #include "MantidKernel/SingletonHolder.h"
+#include "MantidKernel/MultiThreaded.h"
 
 #include <boost/shared_ptr.hpp>
 
+
 namespace Mantid
 {
 
@@ -76,7 +78,13 @@ namespace API
 
     /// Query available functions based on the template type
     template<typename FunctionType>
-    std::vector<std::string> getFunctionNames() const;
+    const std::vector<std::string>& getFunctionNames() const;
+
+    using Kernel::DynamicFactory<IFunction>::subscribe;
+    void subscribe(const std::string& className, AbstractFactory* pAbstractFactory,
+                   Kernel::DynamicFactory<IFunction>::SubscribeAction replace=ErrorIfExists);
+
+    void unsubscribe(const std::string& className);
 
   private:
     friend struct Mantid::Kernel::CreateUsingNew<FunctionFactoryImpl>;
@@ -116,9 +124,11 @@ namespace API
     /// Add a tie to the created function
     void addTie(boost::shared_ptr<IFunction> fun,const Expression& expr)const;
 
-    ///static reference to the logger class
+    /// Reference to the logger class
     Kernel::Logger& g_log;
 
+    mutable std::map<std::string,std::vector<std::string>> m_cachedFunctionNames;
+    mutable Kernel::Mutex m_mutex;
   };
 
   /**
@@ -127,13 +137,20 @@ namespace API
    * @returns A vector of the names of the functions matching the template type 
    */
   template<typename FunctionType>
-  std::vector<std::string> FunctionFactoryImpl::getFunctionNames() const
+  const std::vector<std::string>& FunctionFactoryImpl::getFunctionNames() const
   {
+    Kernel::Mutex::ScopedLock _lock(m_mutex);
+
+    const std::string soughtType(typeid(FunctionType).name());
+    if ( m_cachedFunctionNames.find( soughtType ) != m_cachedFunctionNames.end() )
+    {
+      return m_cachedFunctionNames[soughtType];
+    }
+
+    // Create the entry in the cache and work with it directly
+    std::vector<std::string>& typeNames = m_cachedFunctionNames[soughtType];
     const std::vector<std::string> names = this->getKeys();
-    std::vector<std::string> typeNames;
-    typeNames.reserve(names.size());
-    for( std::vector<std::string>::const_iterator it = names.begin(); 
-         it != names.end(); ++it )
+    for( auto it = names.begin(); it != names.end(); ++it )
     {
       boost::shared_ptr<IFunction> func = this->createFunction(*it);
       if ( func && dynamic_cast<FunctionType*>(func.get()) )
@@ -143,12 +160,13 @@ namespace API
     }
     return typeNames;
   }
-        ///Forward declaration of a specialisation of SingletonHolder for AlgorithmFactoryImpl (needed for dllexport/dllimport) and a typedef for it.
+
+  ///Forward declaration of a specialisation of SingletonHolder for AlgorithmFactoryImpl (needed for dllexport/dllimport) and a typedef for it.
 #ifdef _WIN32
 // this breaks new namespace declaraion rules; need to find a better fix
-        template class MANTID_API_DLL Mantid::Kernel::SingletonHolder<FunctionFactoryImpl>;
+  template class MANTID_API_DLL Mantid::Kernel::SingletonHolder<FunctionFactoryImpl>;
 #endif /* _WIN32 */
-        typedef MANTID_API_DLL Mantid::Kernel::SingletonHolder<FunctionFactoryImpl> FunctionFactory;
+  typedef MANTID_API_DLL Mantid::Kernel::SingletonHolder<FunctionFactoryImpl> FunctionFactory;
 
   /// Convenient typedef for an UpdateNotification
   typedef FunctionFactoryImpl::UpdateNotification FunctionFactoryUpdateNotification;

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

@@ -12,7 +12,6 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include <iostream>
 #include <string>
 
 namespace Mantid

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

@@ -67,6 +67,8 @@ class DLLExport ICatalog
   virtual void getFileLocation(const long long&,std::string& )=0;
   /// get URLs of the files
   virtual void getDownloadURL(const long long& fileid,std::string&)=0;
+  /// get URL of where to PUT (publish) files.
+  virtual const std::string getUploadURL(const std::string &fileName, const std::string &dataFileName)=0;
   /// keep alive
   virtual void keepAlive()=0;
   ///keep alive in minutes

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

@@ -45,9 +45,9 @@ namespace API
 
     /// See the MDHistoWorkspace definition for descriptions of these
     virtual coord_t getInverseVolume() const = 0;
-    virtual signal_t * getSignalArray() = 0;
-    virtual signal_t * getErrorSquaredArray() = 0;
-    virtual signal_t * getNumEventsArray() = 0;
+    virtual signal_t * getSignalArray() const = 0;
+    virtual signal_t * getErrorSquaredArray() const = 0;
+    virtual signal_t * getNumEventsArray() const = 0;
     virtual void setTo(signal_t signal, signal_t errorSquared, signal_t numEvents) = 0;
     virtual Mantid::Kernel::VMD getCenter(size_t linearIndex) const = 0;
     virtual void setSignalAt(size_t index, signal_t value) = 0;

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

@@ -177,6 +177,7 @@ class IMDNode
      * @param length :: length of cylinder below which to integrate
      * @param signal [out] :: set to the integrated signal
      * @param errorSquared [out] :: set to the integrated squared error.
+     * @param signal_fit [out] :: array of values for the fit.
       */
     virtual void integrateCylinder(Mantid::API::CoordTransform & radiusTransform, const coord_t radius, const coord_t length, signal_t & signal, signal_t & errorSquared, std::vector<signal_t> & signal_fit) const = 0;
 

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

@@ -12,7 +12,6 @@
 #include "MantidKernel/Exception.h"
 #include "MantidAPI/WorkspaceGroup.h"
 
-#include <iostream>
 #include <string>
 
 namespace Mantid

Code/Mantid/Framework/API/src/FileLoaderRegistry.cpp

@@ -23,7 +23,7 @@ namespace Mantid
       {
         void apply(Kernel::FileDescriptor & descriptor) { descriptor.resetStreamToStart(); }
       };
-      ///endcond
+      /// @endcond
 
       /**
        * @param filename A string giving a filename
@@ -79,7 +79,7 @@ namespace Mantid
     /**
      * If the name does not exist then it does nothing
      * @param name Name of the algorithm to remove from the search list
-     * @aparam version An optional version to remove. -1 indicates remove all (Default=-1)
+     * @param version An optional version to remove. -1 indicates remove all (Default=-1)
      */
     void FileLoaderRegistryImpl::unsubscribe(const std::string &name, const int version)
     {

Code/Mantid/Framework/API/src/FunctionFactory.cpp

@@ -335,6 +335,20 @@ namespace Mantid
       }
     }
 
+    void FunctionFactoryImpl::subscribe(const std::string& className, AbstractFactory* pAbstractFactory,
+                   Kernel::DynamicFactory<IFunction>::SubscribeAction replace)
+    {
+      // Clear the cache, then do all the work in the base class method
+      m_cachedFunctionNames.clear();
+      Kernel::DynamicFactory<IFunction>::subscribe(className,pAbstractFactory,replace);
+    }
+
+    void FunctionFactoryImpl::unsubscribe(const std::string& className)
+    {
+      // Clear the cache, then do all the work in the base class method
+      m_cachedFunctionNames.clear();
+      Kernel::DynamicFactory<IFunction>::unsubscribe(className);
+    }
 
   } // namespace API
 } // namespace Mantid

Code/Mantid/Framework/API/src/IPowderDiffPeakFunction.cpp

@@ -213,83 +213,6 @@ namespace API
     return;
   }
 
-  //----------------------------------------------------------------------------------------------
-  /** General implementation of the method for all peaks. Limits the peak evaluation to
-   * a certain number of FWHMs around the peak centre. The outside points are set to 0.
-   * Calls functionLocal() to compute the actual values
-   * @param out :: Output function values
-   * @param xValues :: X values for data points
-   * @param nData :: Number of data points
-
-  void IPowderDiffPeakFunction::functionLocal(double* out, const double* xValues, const size_t nData)const
-  {
-    double c = this->centre();
-    double dx = fabs(s_peakRadius*this->fwhm());
-    int i0 = -1;
-    int n = 0;
-    for(size_t i = 0; i < nData; ++i)
-    {
-      if (fabs(xValues[i] - c) < dx)
-      {
-        if (i0 < 0) i0 = static_cast<int>(i);
-        ++n;
-      }
-      else
-      {
-        out[i] = 0.0;
-      }
-    }
-
-    if (i0 < 0 || n == 0)
-      return;
-    this->functionLocal(out+i0, xValues+i0, n);
-
-    return;
-  }
-     */
-
-  //----------------------------------------------------------------------------------------------
-  /** General implementation of the method for all peaks. Calculates derivatives only
-   * for a range of x values limited to a certain number of FWHM around the peak centre.
-   * For the points outside the range all derivatives are set to 0.
-   * Calls functionDerivLocal() to compute the actual values
-   * @param out :: Derivatives
-   * @param xValues :: X values for data points
-   * @param nData :: Number of data points
-
-  void IPowderDiffPeakFunction::functionDeriv1D(Jacobian* out, const double* xValues, const size_t nData) const
-  {
-    double c = this->centre();
-    double dx = fabs(s_peakRadius*this->fwhm());
-    int i0 = -1;
-    int n = 0;
-    for(size_t i = 0; i < nData; ++i)
-    {
-      if (fabs(xValues[i] - c) < dx)
-      {
-        if (i0 < 0) i0 = static_cast<int>(i);
-        ++n;
-      }
-      else
-      {
-        for(size_t ip = 0; ip < this->nParams(); ++ip)
-        {
-          out->set(i,ip, 0.0);
-        }
-      }
-    }
-    if (i0 < 0 || n == 0) return;
-#if 0
-    PartialJacobian1 J(out,i0);
-    this->functionDerivLocal(&J,xValues+i0,n);
-#else
-    throw runtime_error("Need to think how to implement! Message 1026.");
-#endif
-
-    return;
-  }
-   */
-
   //----------------------------------------------------------------------------------------------
   /** Set peak radius
     * @param r :: radius