Merge branch 'feature/8585_EISF_output_from_fitting' of github.com:ma…

…ntidproject/mantid into feature/8585_EISF_output_from_fitting

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/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/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/LogManager.cpp

@@ -87,47 +87,30 @@ Kernel::Logger& LogManager::g_log = Kernel::Logger::get("LogManager");
   const Kernel::DateAndTime LogManager::startTime() const
   {
     const std::string start_prop("start_time");
-    const std::string run_start_prop("run_start");
-    if (this->hasProperty(start_prop))
+    if ( hasProperty(start_prop) )
     {
-      std::string start = this->getProperty(start_prop)->value();
-      if (DateAndTime(start) != DateAndTimeHelpers::GPS_EPOCH)
-      {
-        return DateAndTime(start);
-      }
-      else if (this->hasProperty(run_start_prop))
-      {
-        std::string start = this->getProperty(run_start_prop)->value();
-        if (DateAndTime(start) != DateAndTimeHelpers::GPS_EPOCH)
+      try {
+        DateAndTime start_time(getProperty(start_prop)->value());
+        if (start_time != DateAndTimeHelpers::GPS_EPOCH)
         {
-          return DateAndTime(start);
+          return start_time;
         }
-        else
-        {
-          throw std::runtime_error("Run::startTime() - No start time has been set for this run.");
-        }
-      }
-      else
-      {
-        throw std::runtime_error("Run::startTime() - No start time has been set for this run.");
-      }
-    }
-    else if (this->hasProperty(run_start_prop))
-    {
-      std::string start = this->getProperty(run_start_prop)->value();
-      if (DateAndTime(start) != DateAndTimeHelpers::GPS_EPOCH)
-      {
-        return DateAndTime(start);
-      }
-      else
-      {
-        throw std::runtime_error("Run::startTime() - No start time has been set for this run.");
-      }
+      } catch (std::invalid_argument&) { /*Swallow and move on*/ }
     }
-    else
+
+    const std::string run_start_prop("run_start");
+    if ( hasProperty(run_start_prop) )
     {
-      throw std::runtime_error("Run::startTime() - No start time has been set for this run.");
+      try {
+        DateAndTime start_time(getProperty(run_start_prop)->value());
+        if (start_time != DateAndTimeHelpers::GPS_EPOCH)
+        {
+          return start_time;
+        }
+      } catch (std::invalid_argument&) { /*Swallow and move on*/ }
     }
+
+    throw std::runtime_error("No valid start time has been set for this run.");
   }
 
   /** Return the run end time as given by the 'end_time' or 'run_end' property.
@@ -138,21 +121,22 @@ Kernel::Logger& LogManager::g_log = Kernel::Logger::get("LogManager");
   const Kernel::DateAndTime LogManager::endTime() const
   {
     const std::string end_prop("end_time");
-    const std::string run_end_prop("run_end");
-    if (this->hasProperty(end_prop))
-    {
-      std::string end = this->getProperty(end_prop)->value();
-      return DateAndTime(end);
-    }
-    else if (this->hasProperty(run_end_prop))
+    if ( hasProperty(end_prop) )
     {
-      std::string end = this->getProperty(run_end_prop)->value();
-      return DateAndTime(end);
+      try {
+        return DateAndTime(getProperty(end_prop)->value());
+      } catch (std::invalid_argument&) { /*Swallow and move on*/ }
     }
-    else
+
+    const std::string run_end_prop("run_end");
+    if (hasProperty(run_end_prop))
     {
-      throw std::runtime_error("Run::endTime() - No end time has been set for this run.");
+      try {
+        return DateAndTime(getProperty(run_end_prop)->value());
+      } catch (std::invalid_argument&) { /*Swallow and move on*/ }
     }
+
+    throw std::runtime_error("No valid end time has been set for this run.");
   }
 
 

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

@@ -32,6 +32,9 @@ namespace
   const char * GONIOMETER_LOG_NAME = "goniometer";
   /// Name of the stored histogram bins log when saved to NeXus
   const char * HISTO_BINS_LOG_NAME = "processed_histogram_bins";
+  const char * PEAK_RADIUS_GROUP = "peak_radius";
+  const char * INNER_BKG_RADIUS_GROUP = "inner_bkg_radius";
+  const char * OUTER_BKG_RADIUS_GROUP = "outer_bkg_radius";
 }
 // Get a reference to the logger
 Kernel::Logger& Run::g_log = Kernel::Logger::get("Run");
@@ -358,7 +361,31 @@ Kernel::Logger& Run::g_log = Kernel::Logger::get("Run");
       file->writeData("value", m_histoBins);
       file->closeGroup();
     }
+    if( this->hasProperty("PeakRadius") )
+    {
+    	const std::vector<double> & values =
+    			this->getPropertyValueAsType<std::vector<double> >("PeakRadius");
 
+        file->makeGroup(PEAK_RADIUS_GROUP, "NXdata", 1);
+        file->writeData("value", values);
+        file->closeGroup();
+    }
+    if( this->hasProperty("BackgroundInnerRadius") )
+    {
+        file->makeGroup(INNER_BKG_RADIUS_GROUP, "NXdata", 1);
+       	const std::vector<double> & values =
+        		this->getPropertyValueAsType<std::vector<double> >("BackgroundInnerRadius");
+        file->writeData("value", values);
+        file->closeGroup();
+    }
+    if( this->hasProperty("BackgroundOuterRadius") )
+    {
+        file->makeGroup(OUTER_BKG_RADIUS_GROUP, "NXdata", 1);
+       	const std::vector<double> & values =
+        		this->getPropertyValueAsType<std::vector<double> >("BackgroundOuterRadius");
+        file->writeData("value", values);
+        file->closeGroup();
+    }
     if(!keepOpen)file->closeGroup();
   }
 
@@ -392,6 +419,30 @@ Kernel::Logger& Run::g_log = Kernel::Logger::get("Run");
         file->readData("value",m_histoBins);
         file->closeGroup();
       }
+      else if(name_class.first == PEAK_RADIUS_GROUP)
+      {
+        file->openGroup(name_class.first, "NXdata");
+        std::vector<double> values;
+        file->readData("value",values);
+        file->closeGroup();
+        this->addProperty("PeakRadius",values, true);
+      }
+      else if(name_class.first == INNER_BKG_RADIUS_GROUP)
+      {
+        file->openGroup(name_class.first, "NXdata");
+        std::vector<double> values;
+        file->readData("value",values);
+        file->closeGroup();
+        this->addProperty("BackgroundInnerRadius",values, true);
+      }
+      else if(name_class.first == OUTER_BKG_RADIUS_GROUP)
+      {
+        file->openGroup(name_class.first, "NXdata");
+        std::vector<double> values;
+        file->readData("value",values);
+        file->closeGroup();
+        this->addProperty("BackgroundOuterRadius",values, true);
+      }
       else if (name_class.first == "proton_charge" && !this->hasProperty("proton_charge"))
       {
         // Old files may have a proton_charge field, single value (not even NXlog)