Refs #6550 Added Tilt parameter and 3 output values per peak

Also includes some cpp warning fixes and wiki updates

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

@@ -0,0 +1,49 @@
+/*
+ * SelectionNotificationService.h
+ *
+ *  Created on: Mar 21, 2013
+ *      Author: ruth
+ */
+
+#ifndef SELECTIONNOTIFICATIONSERVICE_H_
+#define SELECTIONNOTIFICATIONSERVICE_H_
+
+
+#include "MantidKernel/DataService.h"
+#include "MantidAPI/DllConfig.h"
+#include "MantidKernel/SingletonHolder.h"
+#include <Poco/AutoPtr.h>
+
+namespace Mantid
+{
+
+namespace API
+{
+
+class  DLLExport SelectionNotificationServiceImpl : public Kernel::DataService<std::vector<double>>
+{
+
+
+
+private:
+
+  /// Constructor
+  SelectionNotificationServiceImpl();
+  /// Private, unimplemented copy constructor
+ // SelectionNotificationServiceImpl(const AnalysisDataServiceImpl&);
+
+  /// Private destructor
+  virtual ~SelectionNotificationServiceImpl(){}
+
+};
+///Forward declaration of a specialisation of SingletonHolder for AnalysisDataServiceImpl (needed for dllexport/dllimport) and a typedef for it.
+#ifdef _WIN32
+  // this breaks new namespace declaraion rules; need to find a better fix
+  template class MANTID_API_DLL Mantid::Kernel::SingletonHolder<SelectionNotificationServiceImpl>;
+#endif /* _WIN32 */
+  typedef MANTID_API_DLL Mantid::Kernel::SingletonHolder<SelectionNotificationServiceImpl> SelectionNotificationService;
+
+} // Namespace API
+} // Namespace Mantid
+
+#endif /* SELECTIONNOTIFICATIONSERVICE_H_ */

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

@@ -0,0 +1,27 @@
+#include "MantidAPI/SelectionNotificationService.h"
+#include "MantidKernel/DataService.h"
+/*
+ * SelectionNotificationService.cpp
+ *
+ *  Created on: Mar 21, 2013
+ *      Author: ruth
+ */
+
+namespace Mantid
+{
+  namespace API
+  {
+
+
+    SelectionNotificationServiceImpl::SelectionNotificationServiceImpl():
+              Mantid::Kernel::DataService<std::vector<double> >("SelectionNotificationService")
+      {
+      }
+
+
+
+  } // Namespace API
+ } // Namespace Mantid
+
+
+

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

@@ -16,6 +16,7 @@
 #include "MantidDataObjects/PeaksWorkspace.h"
 #include "MantidAPI/IFunction.h"
 #include "MantidGeometry/Crystal/OrientedLattice.h"
+#include "MantidKernel/Matrix.h"
 using Mantid::API::IFunction;
 using Mantid::Geometry::Instrument;
 using Mantid::DataObjects::PeaksWorkspace_sptr;
@@ -28,10 +29,28 @@ namespace Mantid
     /** IndexOptimizePeaks
 
      Description:
-     This algorithm basically indexes peaks with the crystal orientation matrix stored in the peaks workspace.
+     This algorithm basically indexes peaks with the sample orientation matrix stored in the peaks workspace.
      The optimization is on the goniometer settings for the runs in the peaks workspace and also the sample
      orientation is optimized.
 
+     Attributes:
+        OptRuns : a list of run numbers whose sample orientations are to be optimized.  The list is separated by /.
+        PeakWorkspaceName : The name of the PeaksWorkspace in the AnalysisDataService
+
+      Parameters:
+        SampleXOffset
+        SampleYOffset
+        SampleZOffset
+        chixxx - xxx is a run number from OptRuns. This is the chi angle in degrees
+        phixxx - xxx is a run number from OptRuns. This is the phi angle in degrees
+        omegaxxx - xxx is a run number from OptRuns. This is the omega angle in degrees
+
+
+      Workspace:
+        For each peak used, there are 3 pieces of Data, one for the h int offset, one for the k int offset and one for
+        the l int offset.  The x Values represent the peak number in the peaks workspace.
+
+
      Copyright © 2012 ISIS Rutherford Appleton Laboratory & NScD Oak Ridge National Laboratory
 
      This file is part of Mantid.
@@ -93,6 +112,10 @@ namespace Mantid
         return (size_t) 2;
       }
 
+     static Kernel::Matrix<double> DerivRotationMatrixAboutRegAxis( double theta, char axis);
+
+     static Kernel::Matrix<double> RotationMatrixAboutRegAxis( double theta, char axis);
+
       boost::shared_ptr<Geometry::Instrument>
           getNewInstrument(DataObjects::PeaksWorkspace_sptr Peaks) const;
 

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

@@ -85,18 +85,20 @@ namespace Mantid
           "Workspace of Results");
 
 
-      declareProperty("IncludeVaryingSampleOffsets", true,
+      declareProperty("AdjustSampleOffsets", true,
           "If true sample offsets will be adjusted to give better fits, otherwise they will be fixed as zero(def=true)");
 
+      declareProperty("OptimizeGoniometerTilt", false, "Set true if main error is due to a tilted Goniometer(def=false)");
+
       declareProperty("Chi2overDoF", -1.0, "chi squared over dof", Direction::Output);
       declareProperty("nPeaks", -1, "Number of Peaks Used", Direction::Output);
       declareProperty("nParams", -1, "Number of Parameters fit", Direction::Output);
 
 
-      declareProperty("ToleranceChiPhiOmega", 5.0, "Max offset in degrees from current settings(def=5)");
+      declareProperty("MaxAngularChange", 5.0, "Max offset in degrees from current settings(def=5)");
 
-      declareProperty("MaxIntHKLOffsetPeaks2Use", .25,
-          "Use only peaks whose h,k,and l offsets from and integer are below this level(def=.25)");
+      declareProperty("MaxIndexingError", .25,
+          "Use only peaks whose fractional hkl values are below this tolerance(def=.25)");
 
       declareProperty(
           "MaxHKLPeaks2Use", -1.0,
@@ -105,15 +107,20 @@ namespace Mantid
           "Maximum Change in Sample position in meters(def=.005)");
 
 
-      setPropertyGroup("ToleranceChiPhiOmega", "Tolerance settings");
+      setPropertyGroup("MaxAngularChange", "Tolerance settings");
 
       setPropertyGroup("MaxSamplePositionChange_meters", "Tolerance settings");
       setPropertyGroup("MaxHKLPeaks2Use", "Tolerance settings");
-      setPropertyGroup("MaxIntHKLOffsetPeaks2Use", "Tolerance settings");
+      setPropertyGroup("MaxIndexingError", "Tolerance settings");
 
-      setPropertySettings("MaxSamplePositionChange_meters",new EnabledWhenProperty("IncludeVaryingSampleOffsets",
+      setPropertySettings("MaxSamplePositionChange_meters",new EnabledWhenProperty("AdjustSampleOffsets",
             Kernel::IS_EQUAL_TO, "1" ));
 
+      //-------- Output values----------------------------------
+      //Sample offset and goniometer tilt. Can be retrieved from tables, but....
+
+
+
     }
 
     void OptimizeCrystalPlacement::exec()
@@ -142,7 +149,7 @@ namespace Mantid
       Mantid::MantidVec &errB = errs.access();
 
       int nPeaksUsed =0;
-      double HKLintOffsetMax= getProperty("MaxIntHKLOffsetPeaks2Use");
+      double HKLintOffsetMax= getProperty("MaxIndexingError");
       double HKLMax=getProperty("MaxHKLPeaks2Use");
       for ( int i = 0; i < Peaks->getNumberPeaks(); i++ )
       {
@@ -183,11 +190,17 @@ namespace Mantid
         xRef.push_back( ( double ) i );
         yvalB.push_back( 0.0 );
         errB.push_back( 1.0 );
+        xRef.push_back( ( double ) i );
+        yvalB.push_back( 0.0 );
+        errB.push_back( 1.0 );
+        xRef.push_back( ( double ) i );
+        yvalB.push_back( 0.0 );
+        errB.push_back( 1.0 );
 
       }
 
       MatrixWorkspace_sptr mwkspc;
-      int N = Peaks->getNumberPeaks();
+      int N = 3*nPeaksUsed;//Peaks->getNumberPeaks();
       mwkspc =  WorkspaceFactory::Instance().create( "Workspace2D" , (size_t) 1 , N , N );
       mwkspc->setX( 0 , pX );
       mwkspc->setData( 0 , yvals , errs );
@@ -230,7 +243,7 @@ namespace Mantid
 
 
       int nParams=3;
-      double DegreeTol=getProperty("ToleranceChiPhiOmega");
+      double DegreeTol=getProperty("MaxAngularChange");
       std::string startConstraint ="";
       for ( size_t i = 0; i < RunNumList.size(); i++ )
       {
@@ -263,11 +276,11 @@ namespace Mantid
       V3D sampPos = instr->getSample()->getPos();
 
       oss<< ",SampleXOffset="<<sampPos.X()<<",SampleYOffset="<<sampPos.Y()<<",SampleZOffset="<<sampPos.Z();
-
+      oss<<",GonRotx=0.0,GonRoty=0.0,GonRotz=0.0";
       double maxSampshift = getProperty("MaxSamplePositionChange_meters");
       oss1 << startConstraint << sampPos.X()-maxSampshift<<"<SampleXOffset<"<<sampPos.X()+maxSampshift<<","<<sampPos.Y()-maxSampshift<<
           "<SampleYOffset<"<<sampPos.Y()+maxSampshift <<","<<sampPos.Z()-maxSampshift<<"<SampleZOffset<" <<sampPos.Z()+maxSampshift;
-
+      oss1<<","<<-DegreeTol<<"<GonRotx<"<<DegreeTol<<","<<-DegreeTol<<"<GonRoty<"<<DegreeTol<<","<<-DegreeTol<<"<GonRotz<"<<DegreeTol;
       FuncArg += oss.str();
       std::string Constr = oss1.str();
 
@@ -288,15 +301,28 @@ namespace Mantid
 
       fit_alg->setProperty( "CreateOutput" , true );
 
-      if( !(bool)getProperty("IncludeVaryingSampleOffsets"))
+      std::string Ties ="";
+      if( !(bool)getProperty("AdjustSampleOffsets"))
       {
-        std::ostringstream oss( std::ostringstream::out );
-        oss.precision( 3 );
-        oss<<"SampleXOffset="<<sampPos.X()<<",SampleYOffset="<<sampPos.Y()<<",SampleZOffset="<<sampPos.Z();
+        std::ostringstream oss3( std::ostringstream::out );
+        oss3.precision( 3 );
 
-        fit_alg->setProperty("Ties",oss.str());
+        oss3<<"SampleXOffset="<<sampPos.X()<<",SampleYOffset="<<sampPos.Y()<<",SampleZOffset="<<sampPos.Z();
+        Ties =oss3.str();
       }
 
+      if( !(bool)getProperty("OptimizeGoniometerTilt"))
+      {
+        if( !Ties.empty())
+           Ties +=",";
+
+        Ties +="GonRotx=0.0,GonRoty=0.0,GonRotz=0.0";
+
+      }
+
+      if( !Ties.empty())
+         fit_alg->setProperty("Ties",Ties);
+
       fit_alg->setProperty( "Output" , "out" );
 
       fit_alg->executeAsChildAlg();
@@ -311,8 +337,10 @@ namespace Mantid
 
       setProperty( "nPeaks", nPeaksUsed) ;
       setProperty("nParams", nParams );
+
       g_log.debug() << "Chi2overDof=" << chisq <<"    # Peaks used="<< nPeaksUsed
                    << "# fitting parameters ="<< nParams << "   dof=" << (nPeaksUsed - nParams) <<std::endl;
+
       ITableWorkspace_sptr RRes = fit_alg->getProperty( "OutputParameters" );
 
       double sigma = sqrt( chisq );
@@ -341,7 +369,7 @@ namespace Mantid
         std::string namee = RRes->getRef<std::string> ( "Name" , prm );
 
         std::string start= namee.substr(0,3);
-        if( start !="chi" && start !="phi" && start !="ome" && start !="Sam")
+        if( start !="chi" && start !="phi" && start !="ome" && start !="Sam" && start!="Gon")
           continue;
 
         double value = RRes->getRef<double>("Value",prm);
@@ -355,11 +383,14 @@ namespace Mantid
       }
 
     //-----------Fix up Resultant workspace return info -------------------
+
       std::string ResultWorkspaceName = getPropertyValue( "FitInfoTable" );
       AnalysisDataService::Instance().addOrReplace( ResultWorkspaceName , RRes );
+
       setPropertyValue( "FitInfoTable" , ResultWorkspaceName );
 
       //----------- update instrument -------------------------
+
       IPeak& peak =Peaks->getPeak(0);
       boost::shared_ptr<const Instrument>OldInstrument = peak.getInstrument();
       boost::shared_ptr<const ParameterMap>pmap_old = OldInstrument->getParameterMap();
@@ -388,6 +419,10 @@ namespace Mantid
       OutPeaks->setInstrument( NewInstrument );
 
 
+      Matrix<double> GonTilt = PeakHKLErrors::RotationMatrixAboutRegAxis( Results["GonRotx"] ,'x')*
+                               PeakHKLErrors::RotationMatrixAboutRegAxis( Results["GonRoty"] ,'y')*
+                               PeakHKLErrors::RotationMatrixAboutRegAxis( Results["GonRotz"] ,'z');
+   /*   std::set<int> RunNums;
       for( std::vector<std::string>::iterator it  =ChRunNumList.begin(); it !=ChRunNumList.end(); ++it)
       {
         std::string runNumStr = *it;
@@ -402,15 +437,56 @@ namespace Mantid
         uniGonio.setRotationAngle( "chi", chi );
         uniGonio.setRotationAngle( "omega", omega) ;
 
-        Matrix<double> GonMatrix = uniGonio.getR();
+        Matrix<double> GonMatrix = GonTilt*uniGonio.getR();
 
         for( int i = 0 ; i < OutPeaks->getNumberPeaks() ; ++i)
           if( OutPeaks->getPeak(i).getRunNumber()== boost::lexical_cast<int>(runNumStr))
             {
                OutPeaks->getPeak( i ).setGoniometerMatrix( GonMatrix );
 
             }
-      }
+          else
+            RunNums.insert( OutPeaks->getPeak(i).getRunNumber());
+
+       }
+     */
+      int prevRunNum = -1;
+      std::map<int, Matrix<double> > MapRunNum2GonMat;
+      std::string OptRun2 ="/"+OptRunNums+"/";
+      for (int i = 0; i < OutPeaks->getNumberPeaks(); ++i)
+      {
+
+        int RunNum = OutPeaks->getPeak(i).getRunNumber();
+        std::string RunNumStr = boost::lexical_cast<std::string>(RunNum);
+        Matrix<double> GonMatrix;
+        if (RunNum == prevRunNum || MapRunNum2GonMat.find(RunNum) != MapRunNum2GonMat.end())
+          GonMatrix = MapRunNum2GonMat[RunNum];
+        else if (OptRun2.find("/" + RunNumStr + "/") < OptRun2.size() - 2)
+        {
+
+          double chi = Results["chi" + RunNumStr];
+          double phi = Results["phi" + RunNumStr];
+          double omega = Results["omega" + RunNumStr];
+
+          Mantid::Geometry::Goniometer uniGonio;
+          uniGonio.makeUniversalGoniometer();
+
+          uniGonio.setRotationAngle("phi", phi);
+          uniGonio.setRotationAngle("chi", chi);
+          uniGonio.setRotationAngle("omega", omega);
+
+          GonMatrix = GonTilt * uniGonio.getR();
+          MapRunNum2GonMat[RunNum] = GonMatrix;
+        }
+        else
+        {
+          GonMatrix = GonTilt * OutPeaks->getPeak(i).getGoniometerMatrix();
+          MapRunNum2GonMat[RunNum] = GonMatrix;
+        }
+
+        OutPeaks->getPeak(i).setGoniometerMatrix( GonMatrix );
+        prevRunNum= RunNum;
+    }
 
 
       std::string OutputPeaksName= getPropertyValue("ModifiedPeaksWorkspace");