Refs #9041 Merging master in to take care of a merge conflict

Conflict occurred in refl_gui.py

Merge branch origin master into 'feature/9041_refl_gui_plotting'

Conflicts:
	Code/Mantid/scripts/Interface/ui/reflectometer/refl_gui.py

Code/Mantid/Framework/API/CMakeLists.txt

@@ -171,6 +171,7 @@ set ( INC_FILES
 	inc/MantidAPI/IBackgroundFunction.h
 	inc/MantidAPI/IBoxControllerIO.h
 	inc/MantidAPI/ICatalog.h
+	inc/MantidAPI/ICatalogInfoService.h
 	inc/MantidAPI/IConstraint.h
 	inc/MantidAPI/ICostFunction.h
 	inc/MantidAPI/IDataItem.h

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

@@ -1,82 +1,73 @@
 #ifndef MANTID_API_ICATLOG_H_
 #define MANTID_API_ICATLOG_H_
+
 #include "MantidAPI/ITableWorkspace.h"
 
 namespace Mantid
 {
+  namespace ICat
+  {
+    class CatalogSearchParam;
+  }
 
-//forward declarations
-namespace ICat
-{
-class CatalogSearchParam;
-}
-
-namespace API
-{
+  namespace API
+  {
+    /**
+     This class creates an interface for information catalogs to support multiple facilities
 
-   /**
-    This class creates an interface for information catalogs to support multiple facilities
+     @author Sofia Antony, ISIS Rutherford Appleton Laboratory
+     @date 23/09/2010
 
-    @author Sofia Antony, ISIS Rutherford Appleton Laboratory
-    @date 23/09/2010
+     Copyright © 2010 ISIS Rutherford Appleton Laboratory & NScD Oak Ridge National Laboratory
 
-    Copyright © 2010 ISIS Rutherford Appleton Laboratory & NScD Oak Ridge National Laboratory
+     This file is part of Mantid.
 
-    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 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.
 
-    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/>.
 
-    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>
+     File change history is stored at: <https://github.com/mantidproject/mantid>.
+     Code Documentation is available at: <http://doxygen.mantidproject.org>
     */
-class DLLExport ICatalog
-{
-public:
-  // virtual destructor
-  virtual ~ICatalog(){};
-  /// method to login to a catalog
-  virtual void login(const std::string&,const std::string&,const std::string&)=0;
-  /// logout from catalog
-  virtual void logout()=0;
-  ///Search investigations
-  virtual void search(const ICat::CatalogSearchParam&,ITableWorkspace_sptr&, const int &,const int &)=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.
-  virtual void getDataSets(const std::string& ,ITableWorkspace_sptr&)=0;
-  /// get datafiles
-  virtual void getDataFiles(const std::string&,ITableWorkspace_sptr &)=0;
-  ///  instrument list
-  virtual void listInstruments(std::vector<std::string>&)=0;
-  /// get investigationtype lists
-  virtual void listInvestigationTypes(std::vector<std::string>&)=0;
-  /// get file locations
-  virtual void getFileLocation(const long long&,std::string&)=0;
-  /// get URLs of the files
-  virtual void getDownloadURL(const long long&,std::string&)=0;
-  /// get URL of where to PUT (publish) files.
-  virtual const std::string getUploadURL(const std::string&,const std::string&,const std::string&)=0;
-  /// keep alive
-  virtual void keepAlive()=0;
-  ///keep alive in minutes
-  virtual int keepAliveinminutes()=0;
-};
+    class DLLExport ICatalog
+    {
+      public:
+        /// Virtual destructor
+        virtual ~ICatalog(){};
+        /// method to login to a catalog
+        virtual void login(const std::string&,const std::string&,const std::string&)=0;
+        /// logout from catalog
+        virtual void logout()=0;
+        ///Search investigations
+        virtual void search(const ICat::CatalogSearchParam&,ITableWorkspace_sptr&, const int &,const int &)=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.
+        virtual void getDataSets(const std::string& ,ITableWorkspace_sptr&)=0;
+        /// get datafiles
+        virtual void getDataFiles(const std::string&,ITableWorkspace_sptr &)=0;
+        ///  instrument list
+        virtual void listInstruments(std::vector<std::string>&)=0;
+        /// get investigationtype lists
+        virtual void listInvestigationTypes(std::vector<std::string>&)=0;
+        /// keep alive
+        virtual void keepAlive()=0;
+    };
 
-typedef boost::shared_ptr<ICatalog> ICatalog_sptr;
-typedef boost::shared_ptr<const ICatalog> ICatalog_const_sptr;
+    typedef boost::shared_ptr<ICatalog> ICatalog_sptr;
+    typedef boost::shared_ptr<const ICatalog> ICatalog_const_sptr;
+  }
 }
-}
-#endif
+
+#endif /*MANTID_API_ICATLOG_H_*/

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

@@ -0,0 +1,55 @@
+#ifndef MANTID_API_ICATLOGINFOSERVICE_H_
+#define MANTID_API_ICATLOGINFOSERVICE_H_
+
+#include "MantidAPI/DllConfig.h"
+
+namespace Mantid
+{
+  namespace API
+  {
+   /**
+    This class is responsible for interfacing with the Information Data Service (IDS)
+    to upload and download files to and from the archives.
+
+    @author Jay Rainey, ISIS Rutherford Appleton Laboratory
+    @date 24/02/2010
+
+    Copyright © 2010 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 ICatalogInfoService
+    {
+      public:
+        // Virtual destructor
+        virtual ~ICatalogInfoService(){};
+        /// Obtain the datafile location string from the archives.
+        virtual const std::string getFileLocation(const long long&)=0;
+        /// Obtain url to download a file from.
+        virtual const std::string getDownloadURL(const long long&)=0;
+        /// Obtain the url to upload a file to.
+        virtual const std::string getUploadURL(const std::string&,const std::string&,const std::string&)=0;
+    };
+
+    typedef boost::shared_ptr<ICatalogInfoService> ICatalogInfoService_sptr;
+    typedef boost::shared_ptr<const ICatalogInfoService> ICatalogInfoService_const_sptr;
+  }
+}
+
+#endif /*MANTID_API_ICATLOGINFOSERVICE_H_*/

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

@@ -92,6 +92,9 @@ namespace API
 
     void transformDimensions(std::vector<double> & scaling, std::vector<double> & offset);
 
+    size_t getNumberTransformsToOriginal() const;
+    size_t getNumberTransformsFromOriginal() const;
+
     // --------------------------------------------------------------------------------------------
     ///@return the vector of the origin (in the original workspace) that corresponds to 0,0,0... in this workspace
     Mantid::Kernel::VMD & getOrigin()

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

@@ -816,9 +816,7 @@ namespace Mantid
 
       if (startProgress >= 0 && endProgress > startProgress && endProgress <= 1.)
       {
-        std::cerr << "progress observer=" << m_progressObserver << "\n";
         alg->addObserver(this->progressObserver());
-        std::cerr << "progress observer=" << m_progressObserver << "\n";
         m_startChildProgress = startProgress;
         m_endChildProgress = endProgress;
       }

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

@@ -973,54 +973,23 @@ double IFunction::convertValue(double value, Kernel::Unit_sptr& outUnit,
                                boost::shared_ptr<const MatrixWorkspace> ws,
                                size_t wsIndex)const
 {
-  double retVal = value;
-  Kernel::Unit_sptr wsUnit = ws->getAxis(0)->unit();
-
-  // if unit required by formula or look-up-table different from ws-unit then 
-  if ( outUnit->unitID().compare(wsUnit->unitID()) != 0 )
+  // only required if formula or look-up-table different from ws unit
+  const auto & wsUnit = ws->getAxis(0)->unit();
+  if ( outUnit->unitID().compare(wsUnit->unitID()) == 0 ) return value;
+
+  // first check if it is possible to do a quick conversion and convert
+  // slight duplication to below to avoid instantiating vector unless necessary
+  double factor(0.0), power(0.0);
+  if (wsUnit->quickConversion(*outUnit,factor,power) )
   {
-    // first check if it is possible to do a quick convertion convert
-    double factor,power;
-    if (wsUnit->quickConversion(*outUnit,factor,power) )
-    {
-      retVal = factor * std::pow(retVal,power);
-    }
-    else
-    {
-      double l1,l2,twoTheta;
-
-      // Get l1, l2 and theta  (see also RemoveBins.calculateDetectorPosition())
-      Instrument_const_sptr instrument = ws->getInstrument();
-      Geometry::IObjComponent_const_sptr sample = instrument->getSample();
-      if (sample == NULL)
-      {
-        g_log.error() << "No sample defined instrument. Cannot convert units for function\n"
-                      << "Ignore convertion."; 
-        return value; 
-      }
-      l1 = instrument->getSource()->getDistance(*sample);
-      Geometry::IDetector_const_sptr det = ws->getDetector(wsIndex);
-      if ( ! det->isMonitor() )
-      {
-        l2 = det->getDistance(*sample);
-        twoTheta = ws->detectorTwoTheta(det);
-      }
-      else  // If this is a monitor then make l1+l2 = source-detector distance and twoTheta=0
-      {
-        l2 = det->getDistance(*(instrument->getSource()));
-        l2 = l2 - l1;
-        twoTheta = 0.0;
-      }
-
-      std::vector<double> endPoint;
-      endPoint.push_back(retVal);
-      std::vector<double> emptyVec;
-      wsUnit->toTOF(endPoint,emptyVec,l1,l2,twoTheta,0,0.0,0.0);
-      outUnit->fromTOF(endPoint,emptyVec,l1,l2,twoTheta,0,0.0,0.0);
-      retVal = endPoint[0];
-    }
-  }  
-  return retVal;
+    return factor * std::pow(value,power);
+  }
+  else
+  {
+    std::vector<double> singleValue(1, value);
+    convertValue(singleValue, outUnit, ws, wsIndex);
+    return singleValue.front();
+  }
 }
 
 /** Convert values from unit defined in workspace (ws) to outUnit
@@ -1035,50 +1004,60 @@ void IFunction::convertValue(std::vector<double>& values, Kernel::Unit_sptr& out
                                boost::shared_ptr<const MatrixWorkspace> ws,
                                size_t wsIndex) const
 {
-  Kernel::Unit_sptr wsUnit = ws->getAxis(0)->unit();
+  // only required if  formula or look-up-table different from ws unit
+  const auto & wsUnit = ws->getAxis(0)->unit();
+  if ( outUnit->unitID().compare(wsUnit->unitID()) == 0 ) return;
 
-  // if unit required by formula or look-up-table different from ws-unit then 
-  if ( outUnit->unitID().compare(wsUnit->unitID()) != 0 )
+  // first check if it is possible to do a quick conversion convert
+  double factor, power;
+  if (wsUnit->quickConversion(*outUnit,factor,power) )
   {
-    // first check if it is possible to do a quick convertion convert
-    double factor,power;
-    if (wsUnit->quickConversion(*outUnit,factor,power) )
+    auto iend = values.end();
+    for(auto itr = values.begin(); itr != iend; ++itr)
+      (*itr) = factor * std::pow(*itr, power);
+  }
+  else
+  {
+    // Get l1, l2 and theta  (see also RemoveBins.calculateDetectorPosition())
+    Instrument_const_sptr instrument = ws->getInstrument();
+    Geometry::IObjComponent_const_sptr sample = instrument->getSample();
+    if (sample == NULL)
     {
-      for (size_t i = 0; i < values.size(); i++)
-        values[i] = factor * std::pow(values[i],power);
+      g_log.error() << "No sample defined instrument. Cannot convert units for function\n"
+          << "Ignore convertion.";
+      return;
     }
-    else
+    double l1 = instrument->getSource()->getDistance(*sample);
+    Geometry::IDetector_const_sptr det = ws->getDetector(wsIndex);
+    double l2(-1.0), twoTheta(0.0);
+    if ( ! det->isMonitor() )
     {
-      double l1,l2,twoTheta;
-
-      // Get l1, l2 and theta  (see also RemoveBins.calculateDetectorPosition())
-      Instrument_const_sptr instrument = ws->getInstrument();
-      Geometry::IObjComponent_const_sptr sample = instrument->getSample();
-      if (sample == NULL)
-      {
-        g_log.error() << "No sample defined instrument. Cannot convert units for function\n"
-                      << "Ignore convertion."; 
-        return; 
-      }
-      l1 = instrument->getSource()->getDistance(*sample);
-      Geometry::IDetector_const_sptr det = ws->getDetector(wsIndex);
-      if ( ! det->isMonitor() )
-      {
-        l2 = det->getDistance(*sample);
-        twoTheta = ws->detectorTwoTheta(det);
-      }
-      else  // If this is a monitor then make l1+l2 = source-detector distance and twoTheta=0
-      {
-        l2 = det->getDistance(*(instrument->getSource()));
-        l2 = l2 - l1;
-        twoTheta = 0.0;
-      }
-
-      std::vector<double> emptyVec;
-      wsUnit->toTOF(values,emptyVec,l1,l2,twoTheta,0,0.0,0.0);
-      outUnit->fromTOF(values,emptyVec,l1,l2,twoTheta,0,0.0,0.0);
+      l2 = det->getDistance(*sample);
+      twoTheta = ws->detectorTwoTheta(det);
     }
-  }  
+    else  // If this is a monitor then make l1+l2 = source-detector distance and twoTheta=0
+    {
+      l2 = det->getDistance(*(instrument->getSource()));
+      l2 = l2 - l1;
+      twoTheta = 0.0;
+    }
+    int emode = static_cast<int>(ws->getEMode());
+    double efixed(0.0);
+    try
+    {
+      efixed = ws->getEFixed(det);
+    }
+    catch(std::exception &)
+    {
+      // assume elastic
+      efixed = 0.0;
+      emode = 0;
+    }
+
+    std::vector<double> emptyVec;
+    wsUnit->toTOF(values, emptyVec, l1, l2, twoTheta, emode, efixed, 0.0);
+    outUnit->fromTOF(values, emptyVec,l1,l2,twoTheta, emode, efixed, 0.0);
+  }
 }
 
 /**