Merge branch 'master' into feature/8802_convolve_option_for_conv_fit

Conflicts:
	Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataAnalysis.ui

Refs #8802

.gitignore

@@ -162,4 +162,8 @@ Desktop.ini
 # Mac OS X Finder
 .DS_Store
 
+# Ctags index files
+.tags
+.tags_sorted_by_file
+
 Code/Mantid/Vates/VatesSimpleGui/ViewWidgets/inc/MantidVatesSimpleGuiViewWidgets/LibHelper.h

Code/Mantid/Build/CMake/DarwinSetup.cmake

@@ -81,6 +81,13 @@ endif ()
 ###########################################################################
 set ( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -m64" )
 set ( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64 -std=c++0x" )
+set ( CMAKE_XCODE_ATTRIBUTE_CLANG_CXX_LANGUAGE_STANDARD "c++0x" )
+
+if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+  set ( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated-register" )
+  set ( CMAKE_XCODE_ATTRIBUTE_OTHER_CPLUSPLUSFLAGS "-Wno-deprecated-register")
+  set ( CMAKE_XCODE_ATTRIBUTE_CLANG_CXX_LIBRARY "libc++" )
+endif()
 
 if( ${CMAKE_C_COMPILER} MATCHES "icc.*$" )
   set ( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -no-intel-extensions" )

Code/Mantid/Build/CMake/GNUSetup.cmake

@@ -6,16 +6,12 @@
 # project settings should be included in the relevant CMakeLists.txt file
 # for that project.
 
-# Get the GCC version
-EXEC_PROGRAM(${CMAKE_CXX_COMPILER} ARGS --version | cut -d \" \" -f 3 OUTPUT_VARIABLE _compiler_output)
-STRING(REGEX REPLACE ".*([0-9]\\.[0-9]\\.[0-9]).*" "\\1" GCC_COMPILER_VERSION ${_compiler_output})
-MESSAGE(STATUS "gcc version: ${GCC_COMPILER_VERSION}")
-
-# Export the GCC compiler version globally
-set(GCC_COMPILER_VERSION ${GCC_COMPILER_VERSION} CACHE INTERNAL "")
+# Set our own compiler version flag from the cmake one and export it globally
+set( GCC_COMPILER_VERSION ${CMAKE_CXX_COMPILER_VERSION} CACHE INTERNAL "")
+message( STATUS "gcc version: ${GCC_COMPILER_VERSION}" )
 
 # Global warning flags.
-set( GNUFLAGS "-Wall -Wextra -Wconversion -Winit-self -Wpointer-arith -Wcast-qual -Wcast-align -fno-common" ) 
+set( GNUFLAGS "-Wall -Wextra -Wconversion -Winit-self -Wpointer-arith -Wcast-qual -Wcast-align -fno-common" )
 # Disable some warnings about deprecated headers and type conversions that
 # we can't do anything about
 # -Wno-deprecated: Do not warn about use of deprecated headers.
@@ -38,4 +34,3 @@ set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${GNUFLAGS}" )
 set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${GNUFLAGS} -Woverloaded-virtual -fno-operator-names -std=c++0x" )
 # Cleanup
 set ( GNUFLAGS )
-

Code/Mantid/Build/Jenkins/buildscript.bat

@@ -8,6 +8,7 @@
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 
 "C:\Program Files (x86)\CMake 2.8\bin\cmake.exe" --version 
+echo %sha1%
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Check the required build configuration

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

@@ -338,6 +338,11 @@ class MANTID_API_DLL Algorithm : public IAlgorithm, public Kernel::PropertyManag
   /// Pointer to the parent history object (if set)
   boost::shared_ptr<AlgorithmHistory> m_parentHistory;
 
+  /// One vector of workspaces for each input workspace property
+  std::vector<WorkspaceVector> m_groups;
+  /// Size of the group(s) being processed
+  size_t m_groupSize;
+
 private:
   /// Private Copy constructor: NO COPY ALLOWED
   Algorithm(const Algorithm&);
@@ -354,6 +359,9 @@ class MANTID_API_DLL Algorithm : public IAlgorithm, public Kernel::PropertyManag
 
   bool executeAsyncImpl(const Poco::Void & i);
 
+  // Report that the algorithm has completed.
+  void reportCompleted(const double& duration, const bool groupProcessing = false);
+
   // --------------------- Private Members -----------------------------------
   /// Poco::ActiveMethod used to implement asynchronous execution.
   Poco::ActiveMethod<bool, Poco::Void, Algorithm, Poco::ActiveStarter<Algorithm>> *m_executeAsync;
@@ -387,14 +395,10 @@ class MANTID_API_DLL Algorithm : public IAlgorithm, public Kernel::PropertyManag
   /// All the WorkspaceProperties that are Output (not inOut). Set in execute()
   std::vector<IWorkspaceProperty *> m_pureOutputWorkspaceProps;
 
-  /// One vector of workspaces for each input workspace property
-  std::vector<WorkspaceVector> m_groups;
   /// Pointer to the WorkspaceGroup (if any) for each input workspace property
   std::vector<boost::shared_ptr<WorkspaceGroup> > m_groupWorkspaces;
   /// If only one input is a group, this is its index. -1 if they are all groups
   int m_singleGroup;
-  /// Size of the group(s) being processed
-  size_t m_groupSize;
   /// All the groups have similar names (group_1, group_2 etc.)
   bool m_groupsHaveSimilarNames;
   /// A non-recursive mutex for thread-safety

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

@@ -78,13 +78,13 @@ namespace Mantid
     Algorithm::Algorithm() :
     PropertyManagerOwner(),
       m_cancel(false),m_parallelException(false), m_log("Algorithm"), g_log(m_log),
+      m_groupSize(0),
       m_executeAsync(NULL),
       m_notificationCenter(NULL),
       m_progressObserver(NULL),
       m_isInitialized(false), m_isExecuted(false),m_isChildAlgorithm(false), m_recordHistoryForChild(false),
       m_alwaysStoreInADS(false),m_runningAsync(false),
-      m_running(false),m_rethrow(false),m_algorithmID(this),
-      m_singleGroup(-1), m_groupSize(0), m_groupsHaveSimilarNames(false)
+      m_running(false), m_rethrow(false), m_algorithmID(this), m_singleGroup(-1), m_groupsHaveSimilarNames(false)
     {
     }
 
@@ -550,6 +550,18 @@ namespace Mantid
         }
       }
 
+      if(trackingHistory())
+      {
+        // count used for defining the algorithm execution order
+        // If history is being recorded we need to count this as a separate algorithm
+        // as the history compares histories by their execution number
+        ++Algorithm::g_execCount;
+
+        //populate history record before execution so we can record child algorithms in it
+        AlgorithmHistory algHist;
+        m_history = boost::make_shared<AlgorithmHistory>(algHist);
+      }
+
       // ----- Check for processing groups -------------
       // default true so that it has the right value at the check below the catch block should checkGroups throw
       bool callProcessGroups = true;
@@ -560,7 +572,22 @@ namespace Mantid
         if (callProcessGroups)
         {
           // This calls this->execute() again on each member of the group.
-          return processGroups();
+          start_time = Mantid::Kernel::DateAndTime::getCurrentTime();
+          // Start a timer
+          Timer timer;
+          // Call the concrete algorithm's exec method
+          const bool completed = processGroups();
+          // Check for a cancellation request in case the concrete algorithm doesn't
+          interruption_point();			
+          // Get how long this algorithm took to run
+          const float duration = timer.elapsed();
+
+          if(completed)
+          {
+            // Log that execution has completed.
+            reportCompleted(duration, true/*indicat that this is for group processing*/);
+          }
+          return completed;
         }
       }
       catch(std::exception& ex)
@@ -593,19 +620,6 @@ namespace Mantid
             Poco::FastMutex::ScopedLock _lock(m_mutex);
             m_running = true;
           }
-
-
-          if(trackingHistory())
-          {
-            // count used for defining the algorithm execution order
-            // If history is being recorded we need to count this as a separate algorithm
-            // as the history compares histories by their execution number
-            ++Algorithm::g_execCount;
-
-            //populate history record before execution so we can record child algorithms in it
-            AlgorithmHistory algHist;
-            m_history = boost::make_shared<AlgorithmHistory>(algHist);
-          }
 
           start_time = Mantid::Kernel::DateAndTime::getCurrentTime();
           // Start a timer
@@ -631,14 +645,9 @@ namespace Mantid
 
           // RJT, 19/3/08: Moved this up from below the catch blocks
           setExecuted(true);
-          if (!m_isChildAlgorithm || m_alwaysStoreInADS)
-          {
-            getLogger().notice() << name() << " successful, Duration "
-              << std::fixed << std::setprecision(2) << duration << " seconds" << std::endl;
-          }
-          else
-            getLogger().debug() << name() << " finished with isChild = " << isChild() << std::endl;
-          m_running = false;
+
+          // Log that execution has completed.
+          reportCompleted(duration);
         }
         catch(std::runtime_error& ex)
         {
@@ -1614,6 +1623,32 @@ namespace Mantid
         if (m_cancel) throw CancelException();
     }
 
+    /**
+    Report that the algorithm has completed.
+    @param duration : Algorithm duration
+    @param groupProcessing : We have been processing via processGroups if true.
+    */
+    void Algorithm::reportCompleted(const double& duration, const bool groupProcessing)
+    {
+      std::string optionalMessage;
+      if(groupProcessing)
+      {
+        optionalMessage = ". Processed as a workspace group";
+      }
+
+      if (!m_isChildAlgorithm || m_alwaysStoreInADS)
+      {
+        getLogger().notice() << name() << " successful, Duration "
+              << std::fixed << std::setprecision(2) << duration << " seconds" << optionalMessage << std::endl;
+      }
+
+      else
+      {
+        getLogger().debug() << name() << " finished with isChild = " << isChild() << std::endl;
+      }
+      m_running = false;
+    }
+
 
 
   } // namespace API

Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/FindPeaks.h

@@ -203,6 +203,8 @@ class DLLExport FindPeaks : public API::Algorithm
 
   /// Minimum peak height
   double m_minHeight;
+  /// Minimum value of peak's observed maximum Y value
+  double m_leastMaxObsY;
 
   /// Start values
   bool m_useObsCentre;

Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/GetDetOffsetsMultiPeaks.h

@@ -150,9 +150,10 @@ class DLLExport GetDetOffsetsMultiPeaks: public API::Algorithm
   std::string m_backType;
   /// Peak profile type
   std::string m_peakType;
+  /// Criterias for fitting peak
   double m_maxChiSq;
   double m_minPeakHeight;
-
+  double m_leastMaxObsY;
   double m_maxOffset;
 
   std::vector<double> m_peakPositions;

Code/Mantid/Framework/Algorithms/src/CheckWorkspacesMatch.cpp

@@ -488,7 +488,6 @@ bool CheckWorkspacesMatch::compareEventWorkspaces(DataObjects::EventWorkspace_co
   }
   else
   {
-    result = "Success!";
     wsmatch = true;
   }
 
@@ -836,27 +835,24 @@ bool CheckWorkspacesMatch::checkRunProperties(const API::Run& run1, const API::R
   }
 
   // Now loop over the individual logs
-  for ( size_t i = 0; i < ws1logs.size(); ++i )
+  bool matched(true);
+  int64_t length(static_cast<int64_t>(ws1logs.size()));
+  PARALLEL_FOR_IF(true)
+  for ( int64_t i = 0; i < length; ++i )
   {
-    // Check the log name
-    if ( ws1logs[i]->name() != ws2logs[i]->name() )
-    {
-      g_log.debug() << "WS1 log " << i << " name: " << ws1logs[i]->name() << "\n";
-      g_log.debug() << "WS2 log " << i << " name: " << ws2logs[i]->name() << "\n";
-      result = "Log name mismatch";
-      return false;
-    }
-
-    // Now check the log entry itself, using the method that gives it back as a string
-    if ( ws1logs[i]->value() != ws2logs[i]->value() )
+    PARALLEL_START_INTERUPT_REGION
+    if (matched)
     {
-      g_log.debug() << "WS1 log " << ws1logs[i]->name() << ": " << ws1logs[i]->value() << "\n";
-      g_log.debug() << "WS2 log " << ws2logs[i]->name() << ": " << ws2logs[i]->value() << "\n";
-      result = "Log value mismatch";
-      return false;
+      if ( *(ws1logs[i]) != *(ws2logs[i]))
+      {
+        matched = false;
+        result = "Log mismatch";
+      }
     }
+    PARALLEL_END_INTERUPT_REGION
   }
-  return true;
+  PARALLEL_CHECK_INTERUPT_REGION
+  return matched;
 }
 
 //------------------------------------------------------------------------------------------------

Code/Mantid/Framework/Algorithms/src/FindPeaks.cpp

@@ -123,6 +123,10 @@ namespace Algorithms
 
     declareProperty("MinimumPeakHeight", DBL_MIN, "Minimum allowed peak height. ");
 
+    declareProperty("MinimumPeakHeightObs", 0.0, "Least value of the maximum observed Y value of a peak within "
+                    "specified region.  If any peak's maximum observed Y value is smaller, then "
+                    "this peak will not be fit.  It is designed for EventWorkspace with integer counts.");
+
     std::vector<std::string> costFuncOptions;
     costFuncOptions.push_back("Chi-Square");
     costFuncOptions.push_back("Rwp");
@@ -255,6 +259,8 @@ namespace Algorithms
 
     m_useObsCentre = getProperty("StartFromObservedPeakCentre");
 
+    m_leastMaxObsY = getProperty("MinimumPeakHeightObs");
+
     return;
   }
 
@@ -890,6 +896,23 @@ namespace Algorithms
     const MantidVec& vecX = input->readX(spectrum);
     const MantidVec& vecY = input->readY(spectrum);
 
+    // Exclude peak with peak counts
+    bool hasHighCounts = false;
+    for (int i = i_min; i <= i_max; ++i)
+      if (vecY[i] > m_leastMaxObsY)
+       {
+        hasHighCounts = true;
+        break;
+      }
+    if (!hasHighCounts)
+    {
+      std::stringstream ess;
+      ess << "Peak supposed at " << vecY[i_centre] << " does not have enough counts as " << m_leastMaxObsY;
+      g_log.debug(ess.str());
+      addNonFitRecord(spectrum);
+      return;
+    }
+
     //-------------------------------------------------------------------------
     // Estimate peak and background parameters for better fitting
     //-------------------------------------------------------------------------

Code/Mantid/Framework/Algorithms/src/GetDetOffsetsMultiPeaks.cpp

@@ -186,6 +186,11 @@ namespace Algorithms
     declareProperty("MaxChiSq", 100., "Maximum chisq value for individual peak fit allowed. (Default: 100)");
 
     declareProperty("MinimumPeakHeight", 2.0, "Minimum value allowed for peak height.");
+
+    declareProperty("MinimumPeakHeightObs", 0.0, "Least value of the maximum observed Y value of a peak within "
+                    "specified region.  If any peak's maximum observed Y value is smaller, then "
+                    "this peak will not be fit.  It is designed for EventWorkspace with integer counts.");
+
     //Disable default gsl error handler (which is to call abort!)
     gsl_set_error_handler_off();
 
@@ -314,6 +319,7 @@ namespace Algorithms
     m_maxChiSq = this->getProperty("MaxChiSq");
     m_minPeakHeight = this->getProperty("MinimumPeakHeight");
     m_maxOffset=getProperty("MaxOffset");
+    m_leastMaxObsY = getProperty("MinimumPeakHeightObs");
 
     // Create output workspaces
     outputW = boost::make_shared<OffsetsWorkspace>(m_inputWS->getInstrument());

Code/Mantid/Framework/Algorithms/src/MaskBinsFromTable.cpp

@@ -48,7 +48,7 @@ namespace Algorithms
     this->declareProperty(new WorkspaceProperty<>("OutputWorkspace","",Direction::Output),
         "Output Workspace with bins masked.");
     this->declareProperty(new WorkspaceProperty<DataObjects::TableWorkspace>("MaskingInformation", "", Direction::Input),
-        "Input TableWorkspace containing parameters, SpectraList, XMin and XMax.");
+        "Input TableWorkspace containing parameters, XMin and XMax and either SprectaList or DetectorIDsList");
 
     return;
   }
@@ -188,7 +188,7 @@ namespace Algorithms
     if (id_xmin < 0 || id_xmax < 0 || id_xmin == id_xmax)
       throw runtime_error("Either Xmin nor Xmax is not given. ");
     if (id_spec == id_dets)
-      throw runtime_error("Neither SpectraList nor DetectorIDList is not given.");
+      throw runtime_error("Neither SpectraList nor DetectorIDList is given.");
     else if (id_dets >= 0)
       m_useDetectorID = true;
     else

Code/Mantid/Framework/Algorithms/test/CheckWorkspacesMatchTest.h

@@ -688,7 +688,7 @@ class CheckWorkspacesMatchTest : public CxxTest::TestSuite
     TS_ASSERT_THROWS_NOTHING( checker.setProperty("Workspace2",ws3) );
 
     TS_ASSERT( checker.execute() );
-    TS_ASSERT_EQUALS( checker.getPropertyValue("Result"), "Log name mismatch" );
+    TS_ASSERT_EQUALS( checker.getPropertyValue("Result"), "Log mismatch" );
 
     Mantid::API::MatrixWorkspace_sptr ws4 = WorkspaceCreationHelper::Create2DWorkspace123(2,2);
     ws4->mutableRun().addLogData(new Mantid::Kernel::PropertyWithValue<int>("Prop1",100));
@@ -697,7 +697,7 @@ class CheckWorkspacesMatchTest : public CxxTest::TestSuite
     TS_ASSERT_THROWS_NOTHING( checker.setProperty("Workspace2",ws4) );
 
     TS_ASSERT( checker.execute() );
-    TS_ASSERT_EQUALS( checker.getPropertyValue("Result"), "Log value mismatch" );
+    TS_ASSERT_EQUALS( checker.getPropertyValue("Result"), "Log mismatch" );
   }
 
   void test_Input_With_Two_Groups_That_Are_The_Same_Matches()