Merge remote-tracking branch 'origin/master' into feature/5421_IDA_ba…

…yes_interface

Conflicts:
	Code/Mantid/MantidQt/CustomInterfaces/CMakeLists.txt
	Code/Mantid/scripts/Inelastic/IndirectBayes.py

Refs #5421

Code/Mantid/Build/CMake/DarwinSetup.cmake

@@ -60,7 +60,6 @@ set ( PVPLUGINS_DIR MantidPlot.app/pvplugins )
 set ( PVPLUGINS_SUBDIR pvplugins ) # Need to tidy these things up!
 
 # Python packages
-set ( PYTHON_PACKAGES_DIR ${CMAKE_LIBRARY_PATH}/Python )
 
 install ( PROGRAMS /Library/Python/${PY_VER}/site-packages/sip.so DESTINATION ${BIN_DIR} )
 # Explicitly specify which PyQt libraries we want because just taking the whole
@@ -75,8 +74,13 @@ install ( FILES /Library/Python/${PY_VER}/site-packages/PyQt4/Qt.so
                 /Library/Python/${PY_VER}/site-packages/PyQt4/__init__.py
           DESTINATION ${BIN_DIR}/PyQt4 )
 install ( DIRECTORY /Library/Python/${PY_VER}/site-packages/PyQt4/uic DESTINATION ${BIN_DIR}/PyQt4 )
-# nxs package
-install ( DIRECTORY ${PYTHON_PACKAGES_DIR}/nxs DESTINATION ${BIN_DIR} )
+
+# Python packages in Third_Party need copying to build directory and the final package
+file ( GLOB THIRDPARTY_PYTHON_PACKAGES ${CMAKE_LIBRARY_PATH}/Python/* )
+foreach ( PYPACKAGE ${THIRDPARTY_PYTHON_PACKAGES} )
+  install ( DIRECTORY ${PYPACKAGE} DESTINATION ${BIN_DIR} )
+  file ( COPY ${PYPACKAGE} DESTINATION ${PROJECT_BINARY_DIR}/bin )
+endforeach( PYPACKAGE )
 
 install ( DIRECTORY ${QT_PLUGINS_DIR}/imageformats DESTINATION MantidPlot.app/Contents/Frameworks/plugins )
 

Code/Mantid/CMakeLists.txt

@@ -184,7 +184,8 @@ if ( ENABLE_CPACK )
       # rhel requirements
       set ( CPACK_RPM_PACKAGE_REQUIRES "boost >= 1.34.1,qt4 >= 4.2,nexus,nexus-python,qwt,gsl,glibc,qwtplot3d-qt4,OpenCASCADE-libs-modelling >= 6.3.0,OpenCASCADE-libs-foundation >= 6.3.0,OpenCASCADE-libs-visualization >= 6.3.0,OpenCASCADE-libs-ocaf >= 6.3.0,OpenCASCADE-libs-ocaf-lite >= 6.3.0,muParser,numpy" )
       set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},poco-crypto,poco-data,poco-mysql,poco-sqlite,poco-odbc,poco-util,poco-xml,poco-zip,poco-net,poco-netssl,poco-foundation,PyQt4,sip" )
-      # scipy & matplotlib (ipython is too low a version to be used)
+      set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},python-ipython >= 1.1.0" )
+      # scipy & matplotlib
       set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},scipy,python-matplotlib" )
       set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},mxml,hdf,hdf5" )
 

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

@@ -80,6 +80,9 @@ namespace Mantid
         m_log.debug() << "Registered '" << nameVersion.first << "' version '" << nameVersion.second << "' as file loader\n";
       }
 
+      /// Unsubscribe a named algorithm and version from the loader registration
+      void unsubscribe(const std::string &name, const int version = -1);
+
       /// Returns the name of an Algorithm that can load the given filename
       const boost::shared_ptr<IAlgorithm> chooseLoader(const std::string &filename) const;
       /// Checks whether the given algorithm can load the file
@@ -121,6 +124,10 @@ namespace Mantid
         }
       };
 
+      /// Remove a named algorithm & version from the given map
+      void removeAlgorithm(const std::string & name, const int version, 
+                           std::multimap<std::string,int> & typedLoaders);
+
       /// The list of names. The index pointed to by LoaderFormat defines a set for that format
       std::vector<std::multimap<std::string,int> > m_names;
       /// Total number of names registered

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

@@ -45,6 +45,8 @@ class DLLExport IBackgroundFunction : public IFunctionWithLocation
   virtual void fit(const std::vector<double>& X,const std::vector<double>& Y) = 0;
 };
 
+typedef boost::shared_ptr<IBackgroundFunction> IBackgroundFunction_sptr;
+
 } // namespace API
 } // namespace Mantid
 

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

@@ -143,6 +143,8 @@ namespace Mantid
 
       /// Empty the values out of all TimeSeriesProperty logs
       void clearTimeSeriesLogs();
+      /// Empty all but the last value out of all TimeSeriesProperty logs
+      void clearOutdatedTimeSeriesLogValues();
 
       /// Save the run to a NeXus file with a given group name
       virtual void saveNexus(::NeXus::File * file, const std::string & group,bool keepOpen=false) const;

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

@@ -550,10 +550,12 @@ They will work as was expected for folders @ref folders-sec.
         
         @param option: flag to set for auto-update, or not. If true, new versions of the path will replace the local file as soon as they are available at the central repository.
         
+        @return int: number of files changed (because of the cascading of folders)
+
         @exception ScriptRepoException : Invalid entry.
                 
     */
-    virtual void setAutoUpdate(const std::string & path, bool option = true) = 0;
+    virtual int setAutoUpdate(const std::string & path, bool option = true) = 0;
 
 
   };

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

@@ -26,6 +26,7 @@
 #include <Poco/SAX/ContentHandler.h>
 #include <Poco/SAX/SAXParser.h>
 #include <Poco/ScopedLock.h>
+#include <nexus/NeXusException.hpp>
 
 using namespace Mantid::Geometry;
 using namespace Mantid::Kernel;
@@ -867,6 +868,8 @@ namespace API
    * @param file :: open NeXus file
    * @param[out] parameterStr :: special string for all the parameters.
    *             Feed that to ExperimentInfo::readParameterMap() after the instrument is done.
+   * @throws Exception::NotFoundError If instrument definition is not in the nexus file and cannot
+   *                                  be loaded from the IDF.
    */
   void ExperimentInfo::loadExperimentInfoNexus(::NeXus::File * file, std::string & parameterStr)
   {
@@ -890,34 +893,50 @@ namespace API
       this->mutableRun().loadNexus(file, "logs");
     }
 
-    // Now the instrument source
-    instrumentXml = "";
-    instrumentName = "";
-
     // Try to get the instrument file
     file->openGroup("instrument", "NXinstrument");
     file->readData("name", instrumentName);
 
+    try {
+      file->openGroup("instrument_xml", "NXnote");
+      file->readData("data", instrumentXml );
+      file->closeGroup();
+    }
+    catch (NeXus::Exception& ex) {
+      // Just carry on - it might not be there (e.g. old-style processed files)
+      g_log.debug(ex.what());
+    }
+
     // We first assume this is a new version file, but if the next step fails we assume its and old version file.
     int version = 1;
     try {
       file->readData("instrument_source", instrumentFilename);
-    } 
-    catch(...) {
+    }
+    catch (NeXus::Exception&) {
       version = 0;
+      // In the old version 'processed' file, this was held at the top level (as was the parameter map)
       file->closeGroup();
-      file->readData("instrument_source", instrumentFilename);
+      try {
+        file->readData("instrument_source", instrumentFilename);
+      }
+      catch (NeXus::Exception& ex) {
+        // Just carry on - it might not be there (e.g. for SNS files)
+        g_log.debug(ex.what());
+      }
     }
 
-    file->openGroup("instrument_parameter_map", "NXnote");
-    file->readData("data", parameterStr);
-    file->closeGroup();
+    try {
+      file->openGroup("instrument_parameter_map", "NXnote");
+      file->readData("data", parameterStr);
+      file->closeGroup();
+    }
+    catch (NeXus::Exception& ex) {
+      // Just carry on - it might not be there (e.g. for SNS files)
+      g_log.debug(ex.what());
+    }
 
-    if (version > 0)
+    if ( version == 1 )
     {
-      file->openGroup("instrument_xml", "NXnote");
-      file->readData("data", instrumentXml );
-      file->closeGroup();
       file->closeGroup();
     }
 
@@ -937,16 +956,14 @@ namespace API
       }
       catch (std::exception & e)
       {
-        g_log.error() << "Error loading instrument IDF file for '" << instrumentName << "'." << std::endl;
-        g_log.error() << e.what() << std::endl;
+        g_log.error() << "Error loading instrument IDF file for '" << instrumentName << "'.\n";
+        g_log.debug() << e.what() << std::endl;
+        throw;
       }
     }
     else
     {
-      // The filename in the file = just bare file.
-      // So Get the full path back to the instrument directory.
-      instrumentFilename = ConfigService::Instance().getInstrumentDirectory() + "/" + instrumentFilename;
-      g_log.debug() << "Using instrument IDF XML text contained in .nxs file." << std::endl;
+      g_log.debug() << "Using instrument IDF XML text contained in nexus file.\n";
     }
 
 

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

@@ -49,6 +49,7 @@ namespace Mantid
           const int version = it->second;
           logger.debug() << "Checking " << name << " version " << version << std::endl;
 
+          // Use static cast for speed. Checks have been done at registration to check the types
           auto alg = boost::static_pointer_cast<FileLoaderType>(factory.create(name, version)); // highest version
           try
           {
@@ -75,6 +76,20 @@ namespace Mantid
     // Public members
     //----------------------------------------------------------------------------------------------
 
+    /**
+     * 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)
+     */
+    void FileLoaderRegistryImpl::unsubscribe(const std::string &name, const int version)
+    {
+      auto iend = m_names.end();
+      for(auto it = m_names.begin(); it != iend; ++it)
+      {
+        removeAlgorithm(name, version, *it);
+      }
+    }
+
     /**
      * Queries each registered algorithm and asks it how confident it is that it can
      * load the given file. The name of the one with the highest confidence is returned.
@@ -161,5 +176,32 @@ namespace Mantid
     {
     }
 
+    /**
+     * @param name A string containing the algorithm name
+     * @param version The version to remove. -1 indicates all instances
+     * @param typedLoaders A map of names to version numbers 
+     **/
+    void FileLoaderRegistryImpl::removeAlgorithm(const std::string & name, const int version, 
+                                                 std::multimap<std::string,int> & typedLoaders)
+    {
+      if(version == -1) // remove all
+      {
+        typedLoaders.erase(name);
+      }
+      else // find the right version
+      {
+        auto range = typedLoaders.equal_range(name);
+        for(auto ritr = range.first; ritr != range.second; ++ritr)
+        {
+          if(ritr->second == version)
+          {
+            typedLoaders.erase(ritr);
+            break;
+          }
+        }
+      }
+    }
+
+
   } // namespace API
 } // namespace Mantid

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

@@ -378,7 +378,22 @@ Kernel::Logger& LogManager::g_log = Kernel::Logger::get("LogManager");
     }
   }
 
-
+  /** Clears out all but the last entry of all logs of type TimeSeriesProperty
+   *  Check the documentation/definition of TimeSeriesProperty::clearOutdated for
+   *  the definition of 'last entry'.
+   */
+  void LogManager::clearOutdatedTimeSeriesLogValues()
+  {
+    auto & props = getProperties();
+    for ( auto it = props.begin(); it != props.end(); ++it)
+    {
+      if ( auto tsp = dynamic_cast<ITimeSeriesProperty*>(*it) )
+      {
+        tsp->clearOutdated();
+      }
+    }
+  }
+
   //--------------------------------------------------------------------------------------------
   /** Save the object to an open NeXus file.
    * @param file :: open NeXus file

Code/Mantid/Framework/API/test/LogManagerTest.h

@@ -259,7 +259,37 @@ class LogManagerTest : public CxxTest::TestSuite
     TS_ASSERT_EQUALS( runInfo.getPropertyValueAsType<int>(intProp), 99 );
   }
 
+  void clearOutdatedTimeSeriesLogValues()
+  {
+    // Set up a Run object with 3 properties in it (1 time series, 2 single value)
+    LogManager runInfo;
+    const std::string stringProp("aStringProp");
+    const std::string stringVal("testing");
+    runInfo.addProperty(stringProp,stringVal);
+    const std::string intProp("anIntProp");
+    runInfo.addProperty(intProp,99);
+    const std::string tspProp("tsp");
+    addTestTimeSeries(runInfo,"tsp");
 
+    // Check it's set up right
+    TS_ASSERT_EQUALS( runInfo.getProperties().size(), 3 );
+    auto tsp = runInfo.getTimeSeriesProperty<double>(tspProp);
+    TS_ASSERT_EQUALS( tsp->realSize(), 10 );
+
+    auto lastTime = tsp->lastTime();
+    auto lastValue = tsp->lastValue();
+
+    // Do the clearing work
+    TS_ASSERT_THROWS_NOTHING( runInfo.clearOutdatedTimeSeriesLogValues() );
+
+    // Check the time-series property has 1 entry, & the others are unchanged
+    TS_ASSERT_EQUALS( runInfo.getProperties().size(), 3 );
+    TS_ASSERT_EQUALS( tsp->realSize(), 1 );
+    TS_ASSERT_EQUALS( tsp->firstTime(), lastTime );
+    TS_ASSERT_EQUALS( tsp->firstValue(), lastValue );
+    TS_ASSERT_EQUALS( runInfo.getPropertyValueAsType<std::string>(stringProp), stringVal );
+    TS_ASSERT_EQUALS( runInfo.getPropertyValueAsType<int>(intProp), 99 );
+  }
 
   /** Save and load to NXS file */
   void test_nexus()

Code/Mantid/Framework/Algorithms/CMakeLists.txt

@@ -104,6 +104,7 @@ set ( SRC_FILES
 	src/FindDetectorsOutsideLimits.cpp
 	src/FindPeaks.cpp
 	src/FindPeakBackground.cpp
+	src/FitPeak.cpp
 	src/FlatPlateAbsorption.cpp
 	src/GeneralisedSecondDifference.cpp
 	src/GenerateEventsFilter.cpp
@@ -327,6 +328,7 @@ set ( INC_FILES
 	inc/MantidAlgorithms/FindDetectorsOutsideLimits.h
 	inc/MantidAlgorithms/FindPeaks.h
 	inc/MantidAlgorithms/FindPeakBackground.h
+	inc/MantidAlgorithms/FitPeak.h
 	inc/MantidAlgorithms/FlatPlateAbsorption.h
 	inc/MantidAlgorithms/GSLFunctions.h
 	inc/MantidAlgorithms/GeneralisedSecondDifference.h
@@ -554,6 +556,7 @@ set ( TEST_FILES
 	FindDetectorsOutsideLimitsTest.h
 	FindPeaksTest.h
 	FindPeakBackgroundTest.h
+	FitPeakTest.h
 	FlatPlateAbsorptionTest.h
 	GenerateEventsFilterTest.h
 	GeneratePeaksTest.h