refs #8614 conflicts between ticket and recent changes to reduction

Merge branch 'master' into bugfix/8614_letReduction

Conflicts:
	Code/Mantid/scripts/Inelastic/CommonFunctions.py
	Code/Mantid/scripts/Inelastic/DirectEnergyConversion.py

Code/Mantid/Build/CMake/VersionNumber.cmake

@@ -1,7 +1,7 @@
 # Set the version number here for MantidVersion and the package filenames
 
 set ( VERSION_MAJOR 3 )
-set ( VERSION_MINOR 0 )
+set ( VERSION_MINOR 1 )
 
 # UNCOMMENT the next 'set' line to 'force' the patch version number to
 # a value (instead of using the count coming out of 'git describe')

Code/Mantid/Build/dev-packages/deb/mantid-developer/mantid-developer-1.0/DEBIAN/control

@@ -1,9 +1,9 @@
 Package: mantid-developer
-Version: 1.0
+Version: 1.1
 Section: main
 Priority: optional
 Architecture: all
-Depends: cmake-qt-gui (>= 2.8.5), build-essential, subversion, libhdf4-dev, libhdf5-serial-dev, libmxml-dev, libgsl0-dev, libopencascade-modeling-dev, libopencascade-foundation-dev, libssl-dev, openssl, libpoco-dev, libpococrypto9-dbg, libpocodata9-dbg, libpocofoundation9-dbg, libpocomysql9-dbg, libpoconet9-dbg, libpoconetssl9-dbg, libpocoodbc9-dbg, libpocosqlite9-dbg, libpocoutil9-dbg, libpocoxml9-dbg, libpocozip9-dbg, python-dev, python-dbg, python-numpy, libmuparser-dev, libnexus0-dev, libqt4-assistant, libqt4-dbus, libqt4-designer, libqt4-dev, libqt4-help, libqt4-network, libqt4-opengl, libqt4-opengl-dev, libqt4-qt3support, libqt4-script, libqt4-scripttools, libqt4-sql, libqt4-sql-mysql, libqt4-svg, libqt4-test, libqt4-webkit, libqt4-xml, libqt4-xmlpatterns, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dbg, python-qt4-dev, qt4-designer, qt4-qmake, python-sip-dbg, python-sip-dev, libqscintilla2-dev, qt4-dev-tools, libboost-signals-dev, libboost-date-time-dev, libboost-regex-dev, libboost-python-dev, git, libgoogle-perftools-dev,texlive-latex-recommended,texlive-latex-extra,texlive-fonts-recommended,dvipng
+Depends: cmake-qt-gui (>= 2.8.5), build-essential, subversion, libhdf4-dev, libhdf5-serial-dev, libmxml-dev, ipython (>= 1.1), libgsl0-dev, libopencascade-modeling-dev, libopencascade-foundation-dev, libssl-dev, openssl, libpoco-dev, libpococrypto9-dbg, libpocodata9-dbg, libpocofoundation9-dbg, libpocomysql9-dbg, libpoconet9-dbg, libpoconetssl9-dbg, libpocoodbc9-dbg, libpocosqlite9-dbg, libpocoutil9-dbg, libpocoxml9-dbg, libpocozip9-dbg, python-dev, python-dbg, python-numpy, python-scipy, libmuparser-dev, libnexus0-dev, libqt4-assistant, libqt4-dbus, libqt4-designer, libqt4-dev, libqt4-help, libqt4-network, libqt4-opengl, libqt4-opengl-dev, libqt4-qt3support, libqt4-script, libqt4-scripttools, libqt4-sql, libqt4-sql-mysql, libqt4-svg, libqt4-test, libqt4-webkit, libqt4-xml, libqt4-xmlpatterns, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dbg, python-qt4-dev, qt4-designer, qt4-qmake, python-sip-dbg, python-sip-dev, libqscintilla2-dev, qt4-dev-tools, libboost-signals-dev, libboost-date-time-dev, libboost-regex-dev, libboost-python-dev, git, libgoogle-perftools-dev,texlive-latex-recommended,texlive-latex-extra,texlive-fonts-recommended,dvipng
 Installed-Size: 0
 Maintainer: Mantid Project
 Description: Installs all packages required for a Mantid developer

Code/Mantid/Build/dev-packages/rpm/mantid-developer/mantid-developer-el6.spec

@@ -1,6 +1,6 @@
 Name:           mantid-developer
 Version:        1.1
-Release:        2%{?dist}
+Release:        4%{?dist}
 Summary:        Meta Package to install dependencies for Mantid Development
 
 Group:          Development/Tools
@@ -18,6 +18,7 @@ Requires: gcc-c++
 Requires: gsl-devel
 Requires: hdf-devel
 Requires: hdf5-devel
+Requires: python-ipython >= 1.1
 Requires: muParser-devel
 Requires: mxml-devel
 Requires: nexus >= 4.2
@@ -33,6 +34,7 @@ Requires: qwt-devel
 Requires: qwtplot3d-qt4-devel
 Requires: redhat-lsb
 Requires: rpmdevtools
+Requires: scipy
 Requires: sip-devel
 Requires: git
 Requires: openssl-devel
@@ -63,6 +65,9 @@ required for Mantid development.
 %files
 
 %changelog
+* Tue Feb 04 2014 Stuart Campbell <campbellsi@ornl.gov>
+- Added scipy and ipython >= 1.1 dependency
+
 * Tue May 07 2013 Stuart Campbell <campbellsi@ornl.gov>
 - Added dvipng and latex for qt-assistant stuff
 - Added software collection dependencies

Code/Mantid/Build/dev-packages/rpm/mantid-developer/mantid-developer-f19.spec

@@ -1,6 +1,6 @@
 Name:           mantid-developer
 Version:        1.2
-Release:        2%{?dist}
+Release:        4%{?dist}
 Summary:        Meta Package to install dependencies for Mantid Development
 
 Group:          Development/Tools
@@ -27,12 +27,14 @@ Requires: OpenCASCADE-devel
 Requires: poco-devel
 Requires: PyQt4-devel
 Requires: python-devel
+Requires: python-ipython
 Requires: qscintilla-devel
 Requires: qt-devel >= 4.6
 Requires: qwt5-qt4-devel
 Requires: qwtplot3d-qt4-devel
 Requires: redhat-lsb
 Requires: rpmdevtools
+Requires: scipy 
 Requires: sip-devel
 Requires: git
 Requires: openssl-devel
@@ -62,6 +64,9 @@ required for Mantid development.
 %files
 
 %changelog
+* Tue Feb 04 2014 Stuart Campbell <campbellsi@ornl.gov>
+- Added scipy and ipython >= 1.1 dependency
+
 * Tue Aug 20 2013 Peter Peterson <petersonpf@ornl.gov>
 - Removed things not necessary for fedora 19.
 

Code/Mantid/Build/dev-packages/rpm/mantid-developer/mantid-developer-f20.spec

@@ -1,6 +1,6 @@
 Name:           mantid-developer
 Version:        1.3
-Release:        3%{?dist}
+Release:        5%{?dist}
 Summary:        Meta Package to install dependencies for Mantid Development
 
 Group:          Development/Tools
@@ -27,13 +27,15 @@ Requires: OCE-devel
 Requires: poco-devel
 Requires: PyQt4-devel
 Requires: python-devel
+Requires: python-ipython
 Requires: python-sphinx
 Requires: qscintilla-devel
 Requires: qt-devel >= 4.6
 Requires: qwt5-qt4-devel
 Requires: qwtplot3d-qt4-devel
 Requires: redhat-lsb
 Requires: rpmdevtools
+Requires: scipy
 Requires: sip-devel
 Requires: git
 Requires: openssl-devel
@@ -63,6 +65,9 @@ required for Mantid development.
 %files
 
 %changelog
+* Tue Feb 04 2014 Stuart Campbell <campbellsi@ornl.gov>
+- Added scipy and ipython >= 1.1 dependency
+
 * Fri Dec 20 2013 Stuart Campbell <campbellsi@ornl.gov>
 - Added python-sphinx
 

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

@@ -120,6 +120,10 @@ namespace API
     void saveExperimentInfoNexus(::NeXus::File * file) const;
     /// Loads an experiment description from the open NeXus file
     void loadExperimentInfoNexus(::NeXus::File * file, std::string & parameterStr);
+    /// Load the instrument from an open NeXus file.
+    void loadInstrumentInfoNexus(::NeXus::File * file, std::string & parameterStr);
+    /// Load the sample and log info from an open NeXus file.
+    void loadSampleAndLogInfoNexus(::NeXus::File * file);
     /// Populate the parameter map given a string
     void readParameterMap(const std::string & parameterStr);
 

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

@@ -50,25 +50,25 @@ class DLLExport ICatalog
   /// logout from catalog
   virtual void logout()=0;
   ///Search investigations
-  virtual void search(const ICat::CatalogSearchParam&,ITableWorkspace_sptr&, const int &offset,const int &limit)=0;
+  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 long long& ,ITableWorkspace_sptr&)=0;
+  virtual void getDataSets(const std::string& ,ITableWorkspace_sptr&)=0;
   /// get datafiles
-  virtual void getDataFiles(const long long&,ITableWorkspace_sptr &)=0;
+  virtual void getDataFiles(const std::string&,ITableWorkspace_sptr &)=0;
   ///  instrument list
-  virtual void listInstruments(std::vector<std::string>& )=0;
+  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;
+  virtual void getFileLocation(const long long&,std::string&)=0;
   /// get URLs of the files
-  virtual void getDownloadURL(const long long& fileid,std::string&)=0;
+  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 &fileName, const std::string &dataFileName)=0;
+  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

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

@@ -864,19 +864,11 @@ namespace API
   }
 
   //--------------------------------------------------------------------------------------------
-  /** Load the object from an open NeXus file.
+  /** Load the sample and log info from an open NeXus file.
    * @param file :: open NeXus file
-   * @param[out] parameterStr :: special string for all the parameters.
-   *             Feed that to ExperimentInfo::readParameterMap() after the instrument is done.
-   * @throws Exception::NotFoundError If instrument definition is not in the nexus file and cannot
-   *                                  be loaded from the IDF.
    */
-  void ExperimentInfo::loadExperimentInfoNexus(::NeXus::File * file, std::string & parameterStr)
+  void ExperimentInfo::loadSampleAndLogInfoNexus(::NeXus::File * file)
   {
-    std::string instrumentName;
-    std::string instrumentXml;
-    std::string instrumentFilename;
-
     // First, the sample and then the logs
     int sampleVersion = mutableSample().loadNexus(file, "sample");
     if (sampleVersion == 0)
@@ -892,6 +884,37 @@ namespace API
       // Newer style: separate "logs" field for the Run object
       this->mutableRun().loadNexus(file, "logs");
     }
+  }
+
+  //--------------------------------------------------------------------------------------------
+  /** Load the object from an open NeXus file.
+   * @param file :: open NeXus file
+   * @param[out] parameterStr :: special string for all the parameters.
+   *             Feed that to ExperimentInfo::readParameterMap() after the instrument is done.
+   * @throws Exception::NotFoundError If instrument definition is not in the nexus file and cannot
+   *                                  be loaded from the IDF.
+   */
+  void ExperimentInfo::loadExperimentInfoNexus(::NeXus::File * file, std::string & parameterStr)
+  {
+    // load sample and log info
+    loadSampleAndLogInfoNexus(file);
+
+    loadInstrumentInfoNexus(file, parameterStr);
+  }
+
+  //--------------------------------------------------------------------------------------------
+  /** Load the instrument from an open NeXus file.
+   * @param file :: open NeXus file
+   * @param[out] parameterStr :: special string for all the parameters.
+   *             Feed that to ExperimentInfo::readParameterMap() after the instrument is done.
+   * @throws Exception::NotFoundError If instrument definition is not in the nexus file and cannot
+   *                                  be loaded from the IDF.
+   */
+  void ExperimentInfo::loadInstrumentInfoNexus(::NeXus::File * file, std::string & parameterStr)
+  {
+    std::string instrumentName;
+    std::string instrumentXml;
+    std::string instrumentFilename;
 
     // Try to get the instrument file
     file->openGroup("instrument", "NXinstrument");
@@ -993,7 +1016,6 @@ namespace API
     }
   }
 
-
   //-------------------------------------------------------------------------------------------------
   /** Parse the result of ParameterMap.asString() into the ParameterMap
    * of the current instrument. The instrument needs to have been loaded

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

@@ -80,12 +80,11 @@ namespace Mantid
         buildBinaryOperationTable(const API::MatrixWorkspace_const_sptr & lhs, const API::MatrixWorkspace_const_sptr & rhs);
 
 
-    private:
+    protected:
       // Overridden Algorithm methods
-      void init();
-      void exec();
+      virtual void exec();
+      virtual void init();
 
-    protected:
       bool handleSpecialDivideMinus();
 
       /// Execution method for event workspaces, to be overridden as needed.

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

@@ -4,9 +4,10 @@
 #include "MantidAPI/Algorithm.h"
 #include "MantidKernel/V3D.h"
 #include <climits>
+#include <list>
+#include <map>
 #include <string>
 #include <vector>
-#include <map>
 
 namespace Mantid
 {
@@ -28,9 +29,9 @@ namespace Algorithms
    
   T.G.Perring June 1990:
   
-  Algorithm is based on a combinateion of Taylor series and
-  assymptotic expansion of the double integral for the
-  efficiency, linearly interpolating betweent the two in 
+  Algorithm is based on a combination of Taylor series and
+  asymptotic expansion of the double integral for the
+  efficiency, linearly interpolating between the two in
   region of common accuracy. Checked against numerical
   integration to yield relative accuracy of 1 part in 10^12
   or better over the entire domain of the input arguments
@@ -49,8 +50,8 @@ namespace Algorithms
 
   These data are not quite consistent, but the errors are small :
     2200 m/s = 25.299 meV
-    5327 barns & 1.4323 cm-1 ==> 10atms ofideal gas at 272.9K
-   but at what temperature are the tubes "10 atms" ?
+    5327 barns & 1.4323 cm-1 ==> 10atms of ideal gas at 272.9K
+   but at what temperature are the tubes at "10 atms" ?
 
   Shall use  1.4323 cm-1 @ 3.49416 A-1 with sigma prop. 1/v
 
@@ -103,9 +104,9 @@ class DLLExport DetectorEfficiencyCor : public API::Algorithm
   /// Calculate one over the wave vector for 2 bin bounds
   double calculateOneOverK(double loBinBound, double uppBinBound) const;
   /// Sets the detector geometry cache if necessary
-  void getDetectorGeometry(boost::shared_ptr<const Geometry::IDetector> det, double & detRadius, Kernel::V3D & detAxis);
+  void getDetectorGeometry(const Geometry::IDetector_const_sptr & det, double & detRadius, Kernel::V3D & detAxis);
   /// Computes the distance to the given shape from a starting point
-  double distToSurface(const Kernel::V3D start, const Geometry::Object *shape) const;
+  double distToSurface(const Kernel::V3D & start, const Geometry::Object *shape) const;
   /// Computes the detector efficiency for a given paramater
   double detectorEfficiency(const double alpha) const;
   /// Computes an approximate expansion of a Chebysev polynomial
@@ -132,24 +133,13 @@ class DLLExport DetectorEfficiencyCor : public API::Algorithm
   /// Sample position
   Kernel::V3D m_samplePos;
   /// The spectra numbers that were skipped
-  std::vector<int64_t> m_spectraSkipped;
+  std::list<int64_t> m_spectraSkipped;
 
 
   // Implement abstract Algorithm methods
   void init();
   void exec();
 
-  ///// Links the energy to the wave number, I got this from Prof T.G.Perring 
-  //const double KSquaredToE;
-  ///// coefficients for Taylor series/assymptotic expansion used at large wavenumbers and large angle
-  //const double c_eff_f[];
-  ///// coefficients for Taylor series/assymptotic expansion used at low wavenumbers and low angle
-  //const double c_eff_g[];
-  ///// the number of coefficients in each of the c_eff_f and c_eff_g arrays
-  //const short NUMCOEFS;
-  ///// constants to use for the ISIS 3He detectors 2.0*sigref*wref/atmref
-  //const double g_helium_prefactor;
-
 };
 
 } // namespace Algorithms

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

@@ -59,6 +59,8 @@ namespace Mantid
     private:
       /// Sets documentation strings for this algorithm
       virtual void initDocs();
+      virtual void init();
+      virtual void exec();
       // Overridden BinaryOperation methods
       void performBinaryOperation(const MantidVec& lhsX, const MantidVec& lhsY, const MantidVec& lhsE,
                                   const MantidVec& rhsY, const MantidVec& rhsE, MantidVec& YOut, MantidVec& EOut);
@@ -80,6 +82,8 @@ namespace Mantid
 
       std::string checkSizeCompatibility(const API::MatrixWorkspace_const_sptr lhs,const API::MatrixWorkspace_const_sptr rhs) const;
 
+      bool m_warnOnZeroDivide;
+
     };
 
   } // namespace Algorithm