Merge branch 'master' into feature/10246_Fix_os10.9_clang_failed_tests

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/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/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/DataHandling/inc/MantidDataHandling/LoadInstrument.h

@@ -94,8 +94,6 @@ namespace Mantid
       /// Algorithm's category for identification overriding a virtual method
       virtual const std::string category() const { return "DataHandling\\Instrument";}
 
-      void execManually();
-
     private:
       void init();
       void exec();

Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadParameterFile.h

@@ -87,8 +87,6 @@ namespace Mantid
       /// Algorithm's category for identification overriding a virtual method
       virtual const std::string category() const { return "DataHandling\\Instrument";}
 
-      static void execManually(bool useString, std::string filename, std::string parameterString, Mantid::API::ExperimentInfo_sptr localWorkspace);
-
     private:
 
       void init();

Code/Mantid/Framework/DataHandling/src/LoadFullprofResolution.cpp

@@ -6,7 +6,6 @@
 #include "MantidGeometry/Instrument.h"
 #include "MantidAPI/InstrumentDataService.h"
 #include "MantidGeometry/Instrument/InstrumentDefinitionParser.h"
-#include "MantidDataHandling/LoadParameterFile.h"
 
 #include <Poco/DOM/DOMWriter.h>
 #include <Poco/DOM/Element.h>
@@ -892,8 +891,10 @@ namespace DataHandling
 
 
     // Load the string into the workspace
-    LoadParameterFile::execManually(true, "", parameterXMLString, ws);
-
+    Algorithm_sptr loadParamAlg = createChildAlgorithm("LoadParameterFile");
+    loadParamAlg->setProperty("ParameterXML", parameterXMLString);
+    loadParamAlg->setProperty("Workspace", ws);
+    loadParamAlg->execute();
   }
 
   /* Add an Ikeda Carpenter PV ALFBE parameter to the XML document according to the table workspace

Code/Mantid/Framework/DataHandling/src/LoadIDFFromNexus.cpp

@@ -2,7 +2,6 @@
 // Includes
 //----------------------------------------------------------------------
 #include "MantidDataHandling/LoadIDFFromNexus.h"
-#include "MantidDataHandling/LoadParameterFile.h"
 #include "MantidKernel/ConfigService.h"
 #include "MantidAPI/FileProperty.h"
 
@@ -86,7 +85,10 @@ void LoadIDFFromNexus::exec()
 
     try {
       // load and also populate instrument parameters from this 'fallback' parameter file 
-      LoadParameterFile::execManually(false, paramFile,"", localWorkspace);
+      Algorithm_sptr loadParamAlg = createChildAlgorithm("LoadParameterFile");
+      loadParamAlg->setProperty("Filename", paramFile);
+      loadParamAlg->setProperty("Workspace", localWorkspace);
+      loadParamAlg->execute();
       g_log.notice() << "Instrument parameter file: " << paramFile << " has been loaded" << std::endl;
     } catch ( std::runtime_error& ) {
       g_log.debug() << "Instrument parameter file: " << paramFile << " not found or un-parsable. ";

Code/Mantid/Framework/DataHandling/src/LoadInstrument.cpp

@@ -5,7 +5,6 @@
 #include "MantidAPI/InstrumentDataService.h"
 #include "MantidAPI/Progress.h"
 #include "MantidDataHandling/LoadInstrument.h"
-#include "MantidDataHandling/LoadParameterFile.h"
 #include "MantidGeometry/Instrument.h"
 #include "MantidGeometry/Instrument/Component.h"
 #include "MantidGeometry/Instrument/Detector.h"
@@ -220,7 +219,10 @@ namespace Mantid
         try
         {
           // To allow the use of ExperimentInfo instead of workspace, we call it manually
-          LoadParameterFile::execManually(false, fullPathParamIDF, "", m_workspace);
+          Algorithm_sptr loadParamAlg = createChildAlgorithm("LoadParameterFile");
+          loadParamAlg->setProperty("Filename", fullPathParamIDF);
+          loadParamAlg->setProperty("Workspace", m_workspace);
+          loadParamAlg->execute();
           g_log.debug("Parameters loaded successfully.");
         } catch (std::invalid_argument& e)
         {

Code/Mantid/Framework/DataHandling/src/LoadParameterFile.cpp

@@ -71,11 +71,11 @@ void LoadParameterFile::init()
 void LoadParameterFile::exec()
 {
   // Retrieve the filename from the properties
-  std::string filename = getPropertyValue("Filename");
+  const std::string filename = getPropertyValue("Filename");
 
   // Retrieve the parameter XML string from the properties
   const Property * const parameterXMLProperty = getProperty("ParameterXML"); // to check whether it is default
-  std::string parameterXML = getPropertyValue("ParameterXML");
+  const std::string parameterXML = getPropertyValue("ParameterXML");
 
   // Check the two properties (at least one must be set)
   if( filename.empty() && parameterXMLProperty->isDefault()){
@@ -85,19 +85,20 @@ void LoadParameterFile::exec()
   // Get the input workspace
   const MatrixWorkspace_sptr localWorkspace = getProperty("Workspace");
 
-  execManually(!parameterXMLProperty->isDefault(), filename, parameterXML, localWorkspace);
-}
-
-void LoadParameterFile::execManually(bool useString, std::string filename, std::string parameterXML,  Mantid::API::ExperimentInfo_sptr localWorkspace)
-{
   // TODO: Refactor to remove the need for the const cast (ticket #8521)
   Instrument_sptr instrument = boost::const_pointer_cast<Instrument>(localWorkspace->getInstrument()->baseInstrument());
 
   // Set up the DOM parser and parse xml file
   DOMParser pParser;
   AutoPtr<Document> pDoc;
 
-  if(useString){
+  //Progress reporting object
+  Progress prog(this, 0.0, 1.0, 100);
+
+  prog.report("Parsing XML");
+  //If we've been given an XML string parse that instead
+  if(!parameterXMLProperty->isDefault())
+  {
     try
     {
       pDoc = pParser.parseString(parameterXML);
@@ -136,11 +137,13 @@ void LoadParameterFile::execManually(bool useString, std::string filename, std::
 
   // Set all parameters that specified in all component-link elements of pRootElem
   InstrumentDefinitionParser loadInstr;
-  loadInstr.setComponentLinks(instrument, pRootElem);
+  loadInstr.setComponentLinks(instrument, pRootElem, &prog);
 
   // populate parameter map of workspace 
   localWorkspace->populateInstrumentParameters();
 
+  prog.resetNumSteps(1, 0.0, 1.0);
+  prog.report("Done");
 }
 
 } // namespace DataHandling

Code/Mantid/Framework/Geometry/inc/MantidGeometry/Instrument/InstrumentDefinitionParser.h

@@ -78,7 +78,7 @@ namespace Geometry
     boost::shared_ptr<Instrument> parseXML(Kernel::ProgressBase * prog);
 
     /// Add/overwrite any parameters specified in instrument with param values specified in <component-link> XML elements
-    void setComponentLinks(boost::shared_ptr<Geometry::Instrument>& instrument, Poco::XML::Element* pElem);
+    void setComponentLinks(boost::shared_ptr<Geometry::Instrument>& instrument, Poco::XML::Element* pElem, Kernel::ProgressBase* progress = NULL);
 
     std::string getMangledName();