Merge remote-tracking branch 'origin/master' into feature/9112_multip…

…le_catalog_support. Refs #9112.

Conflicts:

- Code/Mantid/MantidQt/CustomDialogs/inc/MantidQtCustomDialogs/CatalogPublishDialog.h
- Code/Mantid/MantidQt/CustomDialogs/src/CatalogPublishDialog.cpp

Code/Mantid/Framework/Algorithms/CMakeLists.txt

@@ -189,6 +189,7 @@ set ( SRC_FILES
 	src/SaveGSASInstrumentFile.cpp
 	src/Scale.cpp
 	src/ScaleX.cpp
+	src/SetInstrumentParameter.cpp
 	src/SetUncertainties.cpp
 	src/ShiftLogTime.cpp
 	src/SignalOverError.cpp
@@ -415,6 +416,7 @@ set ( INC_FILES
 	inc/MantidAlgorithms/SaveGSASInstrumentFile.h
 	inc/MantidAlgorithms/Scale.h
 	inc/MantidAlgorithms/ScaleX.h
+	inc/MantidAlgorithms/SetInstrumentParameter.h
 	inc/MantidAlgorithms/SetUncertainties.h
 	inc/MantidAlgorithms/ShiftLogTime.h
 	inc/MantidAlgorithms/SignalOverError.h
@@ -498,10 +500,10 @@ set ( TEST_FILES
 	ConjoinWorkspacesTest.h
 	ConvertAxisByFormulaTest.h
 	ConvertFromDistributionTest.h
+	ConvertMDHistoToMatrixWorkspaceTest.h
 	ConvertSpectrumAxis2Test.h
 	ConvertSpectrumAxisTest.h
 	ConvertTableToMatrixWorkspaceTest.h
-	ConvertMDHistoToMatrixWorkspaceTest.h
 	ConvertToDistributionTest.h
 	ConvertToEventWorkspaceTest.h
 	ConvertToHistogramTest.h
@@ -634,6 +636,7 @@ set ( TEST_FILES
 	SaveGSASInstrumentFileTest.h
 	ScaleTest.h
 	ScaleXTest.h
+	SetInstrumentParameterTest.h
 	ShiftLogTimeTest.h
 	SignalOverErrorTest.h
 	SmoothDataTest.h

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

@@ -95,7 +95,7 @@ class DLLExport CheckWorkspacesMatch : public API::Algorithm
   void doPeaksComparison(API::IPeaksWorkspace_sptr tws1, API::IPeaksWorkspace_sptr tws2);
   void doTableComparison(API::ITableWorkspace_const_sptr tws1, API::ITableWorkspace_const_sptr tws2);
   void doMDComparison(API::Workspace_sptr w1, API::Workspace_sptr w2);
-  bool checkEventLists(DataObjects::EventWorkspace_const_sptr ews1, DataObjects::EventWorkspace_const_sptr ews2);
+  bool compareEventWorkspaces(DataObjects::EventWorkspace_const_sptr ews1, DataObjects::EventWorkspace_const_sptr ews2);
   bool checkData(API::MatrixWorkspace_const_sptr ws1, API::MatrixWorkspace_const_sptr ws2);
   bool checkAxes(API::MatrixWorkspace_const_sptr ws1, API::MatrixWorkspace_const_sptr ws2);
   bool checkSpectraMap(API::MatrixWorkspace_const_sptr ws1, API::MatrixWorkspace_const_sptr ws2);
@@ -104,6 +104,11 @@ class DLLExport CheckWorkspacesMatch : public API::Algorithm
   bool checkSample(const API::Sample& sample1, const API::Sample& sample2);
   bool checkRunProperties(const API::Run& run1, const API::Run& run2); 
 
+  /// Compare 2 EventsList
+  int compareEventsListInDetails(const DataObjects::EventList &el1, const DataObjects::EventList &el2,
+                        double tolTof, double tolWeight, int64_t tolPulse, bool printdetails,
+                        size_t& numdiffpulse, size_t& numdifftof, size_t& numdiffboth) const;
+
   std::string result; ///< the result string
 
   API::Progress * prog;

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

@@ -4,6 +4,7 @@
 #include "MantidAPI/Algorithm.h"
 #include "MantidKernel/System.h"
 #include "MantidDataObjects/OffsetsWorkspace.h"
+#include "MantidDataObjects/EventWorkspace.h"
 #include "MantidDataObjects/TableWorkspace.h"
 #include "MantidAPI/MatrixWorkspace.h"
 #include <gsl/gsl_blas.h>
@@ -15,6 +16,28 @@ namespace Mantid
 {
 namespace Algorithms
 {
+
+struct FitPeakOffsetResult
+{
+	double mask;
+	double offset;
+	double chi2;
+	/// fit sum from GSL optimizer as offset's error
+	double fitSum;
+	/// summation of chi-square
+	double chisqSum;
+	/// Number of peaks with successful fitting
+	double peakPosFittedSize;
+	int numpeakstofit;
+	int numpeaksfitted;
+	int numpeaksindrange;
+	std::string fitoffsetstatus;
+	/// Highest peak position
+	double highestpeakpos;
+	/// Highest peak deviation after calibrated by offset
+	double highestpeakdev;
+};
+
 /**
  Find the offsets for each detector
 
@@ -54,21 +77,78 @@ class DLLExport GetDetOffsetsMultiPeaks: public API::Algorithm
   virtual int version() const { return 1; }
   /// Algorithm's category for identification overriding a virtual method
   virtual const std::string category() const { return "Diffraction"; }
-  /// Call Gaussian as a Child Algorithm to fit the peak in a spectrum
-  int fitSpectra(const int64_t wi, API::MatrixWorkspace_sptr inputW, const std::vector<double> &peakPositions, const std::vector<double> &fitWindows, size_t &nparams,
-                  double &minD, double &maxD,
-                  std::vector<double>&peakPosToFit, std::vector<double> &peakPosFitted, std::vector<double> &chisq);
 
 private:
   /// Sets documentation strings for this algorithm
   virtual void initDocs();
   // Overridden Algorithm methods
   void init();
   void exec();
+
+  void processProperties();
+
+  /// Call Gaussian as a Child Algorithm to fit the peak in a spectrum
+  int fitSpectra(const int64_t wi, API::MatrixWorkspace_sptr inputW, const std::vector<double> &m_peakPositions,
+                 const std::vector<double> &m_fitWindows, size_t &nparams, double &minD, double &maxD,
+                 std::vector<double>&peakPosToFit, std::vector<double> &peakPosFitted, std::vector<double> &chisq,
+                 int &i_highestpeak);
+
+  /// Add peak fitting and offset calculation information to information table workspaces per spectrum
+  void addInfoToReportWS(int wi, FitPeakOffsetResult offsetresult, const std::vector<double> &tofitpeakpositions,
+                         const std::vector<double> &fittedpeakpositions);
+
+  void generatePeaksList(const API::ITableWorkspace_sptr &peakslist,
+                         int wi,
+                         const std::vector<double> &peakPositionRef,
+                         std::vector<double> &peakPosToFit,
+                         std::vector<double> &peakPosFitted,
+                         std::vector<double> &peakHeightFitted, std::vector<double> &chisq, bool useFitWindows,
+                         const std::vector<double> &fitWindowsToUse, const double minD, const double maxD);
+
+  /// Generate output information table workspace
+  Mantid::DataObjects::TableWorkspace_sptr createOutputInfoTable(size_t numspec);
+
+  /// Generate output peak information table workspace
+  Mantid::DataObjects::TableWorkspace_sptr createOutputPeakOffsetTable(size_t numspec);
+
+  FitPeakOffsetResult calculatePeakOffset(const int wi, std::vector<double>& fittedpeakpositions, std::vector<double>& vec_peakPosRef);
+
+  /// Calculate a spectrum's offset by optimizing offset
+  void fitPeaksOffset(const size_t inpnparams, const double minD, const double maxD,
+                      const std::vector<double>& vec_peakPosRef,
+                      const std::vector<double>& vec_peakPosFitted,
+                      const std::vector<double>& vec_fitChi2,
+                      FitPeakOffsetResult& fitresult);
+
+  /// Make a summary on all fit
+  void makeFitSummary();
+
+  /// Remove rows without offset calculated from offset table workspace
+  void removeEmptyRowsFromPeakOffsetTable();
+
+  API::MatrixWorkspace_sptr inputW;
+  DataObjects::EventWorkspace_const_sptr eventW;
+  bool isEvent;
+
   std::string m_backType;
   std::string m_peakType;
   double m_maxChiSq;
   double m_minPeakHeight;
+
+  double maxOffset;
+
+  std::vector<double> m_peakPositions;
+  std::vector<double> m_fitWindows;
+
+  DataObjects::OffsetsWorkspace_sptr outputW;
+  /// Output workspace for debugging purpose
+  DataObjects::OffsetsWorkspace_sptr outputNP;
+  /// Output Mask workspace
+  API::MatrixWorkspace_sptr maskWS;
+
+  DataObjects::TableWorkspace_sptr m_infoTableWS;
+  DataObjects::TableWorkspace_sptr m_peakOffsetTableWS;
+
 };
 
 } // namespace Algorithm

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

@@ -0,0 +1,64 @@
+#ifndef MANTID_ALGORITHMS_SETINSTRUMENTPARAMETER_H_
+#define MANTID_ALGORITHMS_SETINSTRUMENTPARAMETER_H_
+
+#include "MantidKernel/System.h"
+#include "MantidAPI/Algorithm.h"
+
+namespace Mantid
+{
+
+namespace Geometry
+{
+  class ParameterMap;
+  class IComponent;
+}
+
+namespace Algorithms
+{
+
+  /** SetInstrumentParameter : A simple algorithm to add or set the value of an instrument parameter
+    
+    Copyright © 2014 ISIS Rutherford Appleton Laboratory & NScD Oak Ridge National Laboratory
+
+    This file is part of Mantid.
+
+    Mantid is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 3 of the License, or
+    (at your option) any later version.
+
+    Mantid is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+    File change history is stored at: <https://github.com/mantidproject/mantid>
+    Code Documentation is available at: <http://doxygen.mantidproject.org>
+  */
+  class DLLExport SetInstrumentParameter  : public API::Algorithm
+  {
+  public:
+    SetInstrumentParameter();
+    virtual ~SetInstrumentParameter();
+
+    virtual const std::string name() const;
+    virtual int version() const;
+    virtual const std::string category() const;
+
+  private:
+    virtual void initDocs();
+    void init();
+    void exec();
+
+    void addParameter(Mantid::Geometry::ParameterMap& pmap, const Mantid::Geometry::IComponent* cmptId, const std::string& paramName, const std::string& paramType, const std::string& paramValue) const;
+
+  };
+
+
+} // namespace Algorithms
+} // namespace Mantid
+
+#endif  /* MANTID_ALGORITHMS_SETINSTRUMENTPARAMETER_H_ */