Refs #8550. Merge remote-tracking branch 'origin/master' into 8550

Conflicts:
	Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/MuonAnalysis.h

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

@@ -50,7 +50,9 @@ class DLLExport ICatalog
   /// logout from catalog
   virtual void logout()=0;
   ///Search investigations
-  virtual void search(const ICat::CatalogSearchParam&,ITableWorkspace_sptr &)=0;
+  virtual void search(const ICat::CatalogSearchParam&,ITableWorkspace_sptr&, const int &offset,const int &limit)=0;
+  /// Obtain the number of results returned by the search method.
+  virtual int64_t getNumberOfSearchResults(const ICat::CatalogSearchParam&)=0;
   /// search logged in users data
   virtual void myData(ITableWorkspace_sptr &)=0;
   /// get datasets.

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

@@ -55,12 +55,7 @@ namespace API
    */
   ScopedWorkspace::operator bool() const
   {
-    AnalysisDataServiceImpl& ads = AnalysisDataService::Instance();
-
-    if ( ads.doesExist(m_name) )
-      return ads.retrieveWS<Workspace>(m_name);
-    else
-      return false;
+    return AnalysisDataService::Instance().doesExist(m_name);
   }
 
   /**

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

@@ -430,6 +430,17 @@ class AnalysisDataServiceTest : public CxxTest::TestSuite
 
   }
 
+  void test_adding_null_workspace()
+  {
+    auto nullWS = MockWorkspace_sptr();
+
+    // Shouldn't be able to add null pointers
+    TS_ASSERT_THROWS( ads.add("null_workspace", nullWS ), std::runtime_error );
+    TS_ASSERT_THROWS( ads.addOrReplace("null_workspace", nullWS ), std::runtime_error );
+
+    TS_ASSERT( ! ads.doesExist("null_workspace") );
+  }
+
 private:
 
   /// If replace=true then usea addOrReplace

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

@@ -162,6 +162,9 @@ void AsymmetryCalc::exec()
   //Copy the imput time bins on to the output
   outputWS->dataX(0) = inputWS->readX(0);
 
+  // Update Y axis label 
+  outputWS->setYUnitLabel("Asymmetry");
+
   setProperty("OutputWorkspace", outputWS);
 }
 

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

@@ -179,6 +179,9 @@ void MuonRemoveExpDecay::exec()
     PARALLEL_CHECK_INTERUPT_REGION
   }
 
+  // Update Y axis label 
+  outputWS->setYUnitLabel("Asymmetry");
+
   setProperty("OutputWorkspace", outputWS);
 }
 

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

@@ -101,6 +101,30 @@ class AsymmetryCalcTest : public CxxTest::TestSuite
       TS_ASSERT_EQUALS( outputWS->readY(0)[9], -0.5 ); // == (1 - 3)/(1 + 3)
   }
 
+  void test_yUnitLabel()
+  {
+    const std::string outputWSName = "AsymmetryCalcTest_yUnitLabel_OutputWS";
+
+    auto ws = WorkspaceCreationHelper::Create2DWorkspace(2,1);
+
+    AsymmetryCalc alg;
+    alg.initialize();
+    alg.setProperty("InputWorkspace", ws);
+    alg.setProperty("OutputWorkspace", outputWSName);
+    alg.execute();
+
+    auto result = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputWSName);
+
+    TS_ASSERT(result);
+
+    if( result )
+    {
+      TS_ASSERT_EQUALS( result->YUnitLabel(), "Asymmetry" );
+    }
+
+    AnalysisDataService::Instance().remove(outputWSName);
+  }
+
 private:
   AsymmetryCalc asymCalc;
   Mantid::DataHandling::LoadMuonNexus2 loader;

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

@@ -5,8 +5,12 @@
 #include "MantidTestHelpers/WorkspaceCreationHelper.h"
 
 #include "MantidAlgorithms/FindPeaks.h"
+
+#include "MantidAPI/MatrixWorkspace.h"
 #include "MantidDataHandling/LoadNexusProcessed.h"
 #include "MantidDataHandling/LoadInstrument.h"
+#include "MantidDataObjects/Workspace2D.h"
+
 #include <fstream>
 
 using Mantid::Algorithms::FindPeaks;
@@ -65,6 +69,7 @@ class FindPeaksTest : public CxxTest::TestSuite
     TS_ASSERT_DELTA( peaklist->Double(6,1), 1.24, 0.01 );
     TS_ASSERT_DELTA( peaklist->Double(7,1), 1.52, 0.01 );
     TS_ASSERT_DELTA( peaklist->Double(8,1), 2.14, 0.01 );
+
   }
 
   void LoadPG3_733()
@@ -96,4 +101,60 @@ class FindPeaksTest : public CxxTest::TestSuite
 private:
 };
 
+//=================================================================================================
+/** Performance test with large workspaces.
+  */
+
+class FindPeaksTestPerformance : public CxxTest::TestSuite
+{
+  Mantid::API::MatrixWorkspace_sptr m_dataWS;
+
+public:
+  static FindPeaksTestPerformance *createSuite() { return new FindPeaksTestPerformance(); }
+  static void destroySuite( FindPeaksTestPerformance *suite ) { delete suite; }
+
+  /** Constructor
+    */
+  FindPeaksTestPerformance()
+  {
+
+  }
+
+  /** Set up workspaces
+    */
+  void setUp()
+  {
+    // Load data file
+    Mantid::DataHandling::LoadNexusProcessed loader;
+    loader.initialize();
+    loader.setProperty("Filename","focussed.nxs");
+    loader.setProperty("OutputWorkspace", "FindPeaksTest_peaksWS");
+    loader.execute();
+
+    m_dataWS = boost::dynamic_pointer_cast<Mantid::API::MatrixWorkspace>(
+          AnalysisDataService::Instance().retrieve("FindPeaksTest_peaksWS"));
+
+    return;
+  }
+
+  /** Find peaks by auto-determine peaks' positions
+    */
+  void test_FindPeaksAutoPeakPositions()
+  {
+    // Find peaks (Test)
+    FindPeaks finder;
+    if ( !finder.isInitialized() ) finder.initialize();
+
+    if (!m_dataWS)
+      throw std::runtime_error("Unable to get input matrix workspace. ");
+    finder.setPropertyValue("InputWorkspace","FindPeaksTest_peaksWS");
+    finder.setPropertyValue("PeakPositions", "0.8089, 0.9571, 1.0701,1.2356,1.5133,2.1401");
+    finder.setPropertyValue("PeaksList","FindPeaksTest_foundpeaks");
+
+    finder.execute();
+  }
+
+}; // end of class FindPeaksTestPerformance
+
+
 #endif /*FINDPEAKSTEST_H_*/

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

@@ -3,12 +3,14 @@
 
 #include <cxxtest/TestSuite.h>
 
+#include "MantidAPI/AnalysisDataService.h"
+#include "MantidAPI/Workspace.h"
+#include "MantidAlgorithms/RemoveExpDecay.h"
 #include "MantidDataHandling/LoadInstrument.h"
 #include "MantidDataHandling/LoadMuonNexus2.h"
-#include "MantidAlgorithms/RemoveExpDecay.h"
-#include "MantidAPI/Workspace.h"
 #include "MantidDataObjects/Workspace2D.h"
-#include "MantidAPI/AnalysisDataService.h"
+#include "MantidTestHelpers/WorkspaceCreationHelper.h"
+
 #include <stdexcept>
 
 using namespace Mantid::Algorithms;
@@ -90,6 +92,30 @@ class RemoveExpDecayTest : public CxxTest::TestSuite
     }
   }
 
+  void test_yUnitLabel()
+  {
+    const std::string outputWSName = "RemoveExpDecayTest_yUnitLabel_OutputWS";
+
+    auto ws = WorkspaceCreationHelper::Create2DWorkspace(1,1);
+
+    MuonRemoveExpDecay alg;
+    alg.initialize();
+    alg.setProperty("InputWorkspace", ws);
+    alg.setProperty("OutputWorkspace", outputWSName);
+    alg.execute();
+
+    auto result = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputWSName);
+
+    TS_ASSERT(result);
+
+    if( result )
+    {
+      TS_ASSERT_EQUALS( result->YUnitLabel(), "Asymmetry" );
+    }
+
+    AnalysisDataService::Instance().remove(outputWSName);
+  }
+
 
 private:
   MuonRemoveExpDecay alg;

Code/Mantid/Framework/Crystal/CMakeLists.txt

@@ -25,6 +25,7 @@ set ( SRC_FILES
 	src/NormaliseVanadium.cpp
 	src/OptimizeCrystalPlacement.cpp
 	src/OptimizeExtinctionParameters.cpp
+	src/OptimizeLatticeForCellType.cpp
 	src/PeakHKLErrors.cpp
 	src/PeakIntegration.cpp
 	src/PeakIntensityVsRadius.cpp
@@ -80,6 +81,7 @@ set ( INC_FILES
 	inc/MantidCrystal/NormaliseVanadium.h
 	inc/MantidCrystal/OptimizeCrystalPlacement.h
 	inc/MantidCrystal/OptimizeExtinctionParameters.h
+	inc/MantidCrystal/OptimizeLatticeForCellType.h
 	inc/MantidCrystal/PeakHKLErrors.h
 	inc/MantidCrystal/PeakIntegration.h
 	inc/MantidCrystal/PeakIntensityVsRadius.h
@@ -132,6 +134,7 @@ set ( TEST_FILES
 	MaskPeaksWorkspaceTest.h
 	NormaliseVanadiumTest.h
 	OptimizeCrystalPlacementTest.h
+	OptimizeLatticeForCellTypeTest.h
 	PeakHKLErrorsTest.h
 	PeakIntegrationTest.h
 	PeakIntensityVsRadiusTest.h

Code/Mantid/Framework/Crystal/inc/MantidCrystal/LoadIsawPeaks.h

@@ -49,6 +49,7 @@ namespace Crystal
     std::string readHeader( Mantid::DataObjects::PeaksWorkspace_sptr outWS, std::ifstream& in,double &T0 );
 
     void appendFile( Mantid::DataObjects::PeaksWorkspace_sptr outWS, std::string filename);
+    void checkNumberPeaks( Mantid::DataObjects::PeaksWorkspace_sptr outWS, std::string filename );
 
   };
 

Code/Mantid/Framework/Crystal/inc/MantidCrystal/OptimizeLatticeForCellType.h

@@ -0,0 +1,73 @@
+#ifndef MANTID_CRYSTAL_OptimizeLatticeForCellType_H_
+#define MANTID_CRYSTAL_OptimizeLatticeForCellType_H_
+
+#include "MantidAPI/Algorithm.h"
+#include "MantidKernel/System.h"
+#include "MantidDataObjects/OffsetsWorkspace.h"
+#include "MantidDataObjects/PeaksWorkspace.h"
+#include <gsl/gsl_blas.h>
+#include <gsl/gsl_multifit_nlin.h>
+#include <gsl/gsl_multimin.h>
+#include <gsl/gsl_statistics.h>
+
+namespace Mantid
+{
+namespace Crystal
+{
+/**
+ Find the offsets for each detector
+
+ @author Vickie Lynch, SNS
+ @date 02/06/2012
+
+ Copyright &copy; 2009 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 OptimizeLatticeForCellType: public API::Algorithm
+{
+public:
+  /// Default constructorMatrix
+  OptimizeLatticeForCellType();
+  /// Destructor
+  virtual ~OptimizeLatticeForCellType();
+  /// Algorithm's name for identification overriding a virtual method
+  virtual const std::string name() const { return "OptimizeLatticeForCellType"; }
+  /// Algorithm's version for identification overriding a virtual method
+  virtual int version() const { return 1; }
+  /// Algorithm's category for identification overriding a virtual method
+  virtual const std::string category() const { return "Crystal"; }
+  /// Call TOFLattice as a Child Algorithm to get statistics of the peaks
+  double optLattice(std::string inname, std::string cell_type, std::vector<double> & params);
+
+private:
+  /// Sets documentation strings for this algorithm
+  virtual void initDocs();
+  // Overridden Algorithm methods
+  void init();
+  void exec();
+  /// Static reference to the logger class
+  static Kernel::Logger& g_log;
+
+};
+
+} // namespace Algorithm
+} // namespace Mantid
+
+#endif /*MANTID_CRYSTAL_OptimizeLatticeForCellType_H_*/

Code/Mantid/Framework/Crystal/src/LoadIsawPeaks.cpp

@@ -584,8 +584,29 @@ namespace Crystal
     }
 
   }
+  //-----------------------------------------------------------------------------------------------
+  /** Count the peaks from a .peaks file and compare with the workspace
+   * @param outWS :: the workspace in which to place the information
+   * @param filename :: path to the .peaks file
+   */
+  void LoadIsawPeaks::checkNumberPeaks( PeaksWorkspace_sptr outWS, std::string filename )
+  {
 
-
+    // Open the file
+    std::ifstream in( filename.c_str() );
+    std::string first;
+    int NumberPeaks = 0;
+    while (getline(in,first))
+    {
+    	if (first[0] == '3')NumberPeaks++;
+    }
+    if(NumberPeaks != outWS->getNumberPeaks())
+    {
+      g_log.error()<<"Number of peaks in file is " << NumberPeaks << " but only read "
+    		  <<outWS->getNumberPeaks() << std::endl;
+      throw std::length_error("Wrong number of peaks read");
+    }
+  }
 
   //----------------------------------------------------------------------------------------------
   /** Execute the algorithm.
@@ -600,6 +621,8 @@ namespace Crystal
 
     // Save it in the output
     setProperty("OutputWorkspace", boost::dynamic_pointer_cast<Workspace>(ws));
+
+    this->checkNumberPeaks(ws, getPropertyValue("Filename"));
   }