Merge 'origin/master' into feature/8538_icat_publish_dois. Refs #8538.

Conflicts:

- Code/Mantid/Framework/ICat/src/ICat4/ICat4Catalog.cpp

CONTRIBUTING.md

@@ -1,6 +1,6 @@
 The [developer documentation](http://www.mantidproject.org/Category:Development) has information on how to participate in the mantid project as a developer. This document is meant to outline the steps for contributing to mantid without becomming a developer.
 
- 1. Fork the repository.
+ 1. [Fork](https://help.github.com/articles/fork-a-repo) the repository.
  2. Make changes as you see fit. Please still follow the guidelines for [running the unit tests](http://www.mantidproject.org/Running_the_unit_tests) and the [build servers](http://www.mantidproject.org/The_automated_build_process).
  3. Before submitting pull requests email mantid-help@mantidproject.org, and a developer will set up a branch that you can submit pull requests to.
  4. Submit a [pull request](https://help.github.com/articles/using-pull-requests) to this branch.

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

@@ -1,6 +1,6 @@
 Name:           mantid-developer
 Version:        1.3
-Release:        6%{?dist}
+Release:        7%{?dist}
 Summary:        Meta Package to install dependencies for Mantid Development
 
 Group:          Development/Tools
@@ -40,6 +40,9 @@ Requires: sip-devel
 Requires: git
 Requires: openssl-devel
 Requires: texlive-latex
+Requires: texlive-latex-bin
+Requires: texlive-was
+Requires: tex-preview
 Requires: dvipng
 Requires: qt-devel
 Requires: qt-assistant
@@ -66,6 +69,9 @@ required for Mantid development.
 %files
 
 %changelog
+* Fri Apr 25 2014 Michael Reuter <reuterma@ornl.gov>
+- Added texlive-latex-bin, texlive-was, tex-preview
+
 * Thu Apr 10 2014 Peter Peterson <petersonpf@ornl.gov>
 - Added qtwebkit-devel
 

Code/Mantid/CMakeLists.txt

@@ -218,18 +218,28 @@ if ( ENABLE_CPACK )
       endif ( ${UNIX_DIST} MATCHES "RedHatEnterprise" )
 
       if( ${UNIX_DIST} STREQUAL "Ubuntu" )
+        # common packages
+        set ( DEPENDS_LIST "libboost-date-time${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION},"
+                           "libboost-regex${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION},"
+                           "libboost-python${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION},"
+                           "libpocofoundation9,libpocoutil9,libpoconet9,libpoconetssl9,libpococrypto9,libpocoxml9,"
+                           "libnexus0 (>= 4.3),libgsl0ldbl,libqtcore4 (>= 4.2),libqtgui4 (>= 4.2),libqt4-opengl (>= 4.2),"
+                           "libqt4-xml (>= 4.2),libqt4-svg (>= 4.2),libqt4-qt3support (>= 4.2),qt4-dev-tools,"
+                           "libqwt5-qt4,libqwtplot3d-qt4-0,python-numpy,python-sip,python-qt4" )
         if( ${UNIX_CODENAME} STREQUAL "lucid" )
-          set ( CPACK_DEBIAN_PACKAGE_DEPENDS "libboost-date-time1.40.0,libboost-regex1.40.0,libpocofoundation9,libpocoutil9,libpoconet9,libpoconetssl9,libpococrypto9,libpocoxml9,libnexus0 (>= 4.3),libgsl0ldbl,libqtcore4 (>= 4.2),libqtgui4 (>= 4.2),libqt4-opengl (>= 4.2),libqt4-xml (>= 4.2),libqt4-svg (>= 4.2),libqt4-qt3support (>= 4.2),libqscintilla2-5,libqwt5-qt4,libqwtplot3d-qt4-0" )
-          set ( CPACK_DEBIAN_PACKAGE_DEPENDS "${CPACK_DEBIAN_PACKAGE_DEPENDS},libopencascade-foundation-6.3.0 (>= 6.3.0),libopencascade-modeling-6.3.0 (>= 6.3.0),libmuparser0,python-numpy,python-sip,python-qt4,libboost-python${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION}" )
+          list ( APPEND DEPENDS_LIST ",libqscintilla2-5,"
+                                     "libopencascade-foundation-6.3.0 (>= 6.3.0),libopencascade-modeling-6.3.0 (>= 6.3.0),"
+                                     "libmuparser0" )
         elseif( ${UNIX_CODENAME} STREQUAL "precise" )
-          set ( CPACK_DEBIAN_PACKAGE_DEPENDS "libboost-date-time1.46.1,libboost-regex1.46.1,libpocofoundation9,libpocoutil9,libpoconet9,libpoconetssl9,libpococrypto9,libpocoxml9,libnexus0 (>= 4.3),python-nxs (>= 4.3),libgsl0ldbl,libqtcore4 (>= 4.2),libqtgui4 (>= 4.2),libqt4-opengl (>= 4.2),libqt4-xml (>= 4.2),libqt4-svg (>= 4.2),libqt4-qt3support (>= 4.2),libqscintilla2-8,libqwt5-qt4,libqwtplot3d-qt4-0" )
-          set ( CPACK_DEBIAN_PACKAGE_DEPENDS "${CPACK_DEBIAN_PACKAGE_DEPENDS},libopencascade-foundation-6.5.0 (>= 6.5.0),libopencascade-modeling-6.5.0 (>= 6.5.0),libmuparser0debian1,python-numpy,python-sip,python-qt4,libboost-python${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION}" )
-          # scipy, matplotlib & ipython
-          set ( CPACK_DEBIAN_PACKAGE_DEPENDS "${CPACK_DEBIAN_PACKAGE_DEPENDS},ipython-qtconsole (>= 1.1),python-matplotlib,python-scipy" )
+          list ( APPEND DEPENDS_LIST ",libqscintilla2-8,"
+                                     "libopencascade-foundation-6.5.0 (>= 6.5.0),libopencascade-modeling-6.5.0 (>= 6.5.0),"
+                                     "libmuparser0debian1,"
+                                     "ipython-qtconsole (>= 1.1),python-matplotlib,python-scipy" )
         else()
           message( WARNING "Mantid does not support packaging of this Ubuntu version: ${UNIX_CODENAME}")
         endif()
-        set ( CPACK_DEBIAN_PACKAGE_DEPENDS "${CPACK_DEBIAN_PACKAGE_DEPENDS},qt4-dev-tools" ) # for qt assistant
+        # parse list to string required for deb package
+        string ( REPLACE ";" "" CPACK_DEBIAN_PACKAGE_DEPENDS ${DEPENDS_LIST} )
       endif()
       # soft requirement of tcmalloc - if built with it, then require it
       IF ( USE_TCMALLOC AND TCMALLOC_FOUND )

Code/Mantid/Framework/API/CMakeLists.txt

@@ -192,7 +192,6 @@ set ( INC_FILES
 	inc/MantidAPI/IFunction1D.h
 	inc/MantidAPI/IFunctionMD.h
 	inc/MantidAPI/IFunctionMW.h
-	inc/MantidAPI/IFunctionValues.h
 	inc/MantidAPI/IFunctionWithLocation.h
 	inc/MantidAPI/ILiveListener.h
 	inc/MantidAPI/IMDEventWorkspace.h

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

@@ -83,6 +83,9 @@ class MANTID_API_DLL Axis
   /// @param index :: The index
   /// @param value :: The new value
   virtual void setValue(const std::size_t& index, const double& value) = 0;
+  /// Find the index of the given double value
+  virtual size_t indexOfValue(const double value) const = 0;
+
   /// Get the spectrum index
   virtual specid_t spectraNo(const std::size_t& index) const;
 

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

@@ -6,7 +6,6 @@
 //----------------------------------------------------------------------
 #include "MantidAPI/DllConfig.h"
 #include "MantidAPI/FunctionDomain.h"
-#include "MantidAPI/IFunctionValues.h"
 
 #include <vector>
 
@@ -40,7 +39,7 @@ namespace API
     File change history is stored at: <https://github.com/mantidproject/mantid>.
     Code Documentation is available at: <http://doxygen.mantidproject.org>
 */
-class MANTID_API_DLL FunctionValues: public IFunctionValues
+class MANTID_API_DLL FunctionValues
 {
 public:
   /// Default constructor.

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

@@ -14,7 +14,7 @@ namespace Mantid
   namespace API
   {
     class FunctionDomain;
-    class IFunctionValues;
+    class FunctionValues;
     class Workspace;
   }
 
@@ -82,7 +82,7 @@ namespace Mantid
       ///   for the data from index i0 to the end of the container.
       virtual void createDomain(
         boost::shared_ptr<API::FunctionDomain>& domain, 
-        boost::shared_ptr<API::IFunctionValues>& values,
+        boost::shared_ptr<API::FunctionValues>& values,
         size_t i0 = 0) = 0;
 
        /// Create an output workspace filled with data simulated with the fitting function.
@@ -97,14 +97,13 @@ namespace Mantid
         const std::string& baseName,
         API::IFunction_sptr function,
         boost::shared_ptr<API::FunctionDomain> domain,
-        boost::shared_ptr<API::IFunctionValues> values,
+        boost::shared_ptr<API::FunctionValues> values,
         const std::string& outputWorkspacePropertyName = "OutputWorkspace"
         ) 
       {
         UNUSED_ARG(baseName);UNUSED_ARG(function);UNUSED_ARG(domain);UNUSED_ARG(values);UNUSED_ARG(outputWorkspacePropertyName);
         throw std::logic_error("Method createOutputWorkspace() isn't implemented");
       }
-
       /// Initialize the function
       /// @param function :: A function to initialize.
       virtual void initFunction(API::IFunction_sptr function);

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

@@ -270,7 +270,7 @@ class MANTID_API_DLL IFunction
   //---------------------------------------------------------//
 
   /// Constructor
-  IFunction():m_isParallel(false),m_handler(NULL), m_progReporter(NULL) {}
+  IFunction():m_isParallel(false),m_handler(NULL), m_progReporter(NULL), m_chiSquared(0.0) {}
   /// Virtual destructor
   virtual ~IFunction();
 
@@ -433,6 +433,14 @@ class MANTID_API_DLL IFunction
 
   /// Calculate numerical derivatives
   void calNumericalDeriv(const FunctionDomain& domain, Jacobian& out);
+  /// Set the covariance matrix
+  void setCovarianceMatrix(boost::shared_ptr<Kernel::Matrix<double>> covar);
+  /// Get the covariance matrix
+  boost::shared_ptr<const Kernel::Matrix<double>> getCovarianceMatrix()const{return m_covar;}
+  /// Set the chi^2
+  void setChiSquared(double chi2) {m_chiSquared = chi2;}
+  /// Get the chi^2
+  double getChiSquared() const {return m_chiSquared;}
 
   /// Set the parallel hint
   void setParallel(bool on) {m_isParallel = on;}
@@ -488,6 +496,10 @@ class MANTID_API_DLL IFunction
 private:
   /// The declared attributes
   std::map<std::string, API::IFunction::Attribute> m_attrs;
+  /// The covariance matrix of the fitting parameters
+  boost::shared_ptr<Kernel::Matrix<double>> m_covar;
+  /// The chi-squared of the last fit
+  double m_chiSquared;
 };
 
 ///shared pointer to the function base class

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

@@ -59,6 +59,7 @@ class MANTID_API_DLL NumericAxis: public Axis
   virtual double operator()(const std::size_t& index, const std::size_t& verticalIndex = 0) const;
   /// Set the value at a specific index
   virtual void setValue(const std::size_t& index, const double& value);
+  size_t indexOfValue(const double value) const;
   virtual bool operator==(const Axis&) const;
   std::string label(const std::size_t& index)const;
   /// Create bin boundaries from the point values

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

@@ -57,6 +57,7 @@ class MANTID_API_DLL SpectraAxis: public Axis
   virtual bool isSpectra() const{return true;}
   virtual double operator()(const std::size_t& index, const std::size_t& verticalIndex = 0) const;
   virtual void setValue(const std::size_t& index, const double& value);
+  size_t indexOfValue(const double value) const;
   virtual bool operator==(const Axis&) const;
   std::string label(const std::size_t& index)const;
 

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

@@ -64,6 +64,8 @@ class MANTID_API_DLL TextAxis: public Axis
   virtual double operator()(const std::size_t& index, const std::size_t& verticalIndex = 0) const;
   /// Set the value at the specified index
   virtual void setValue(const std::size_t& index, const double& value);
+  size_t indexOfValue(const double value) const;
+
   virtual bool operator==(const Axis&) const;
   /// Get the label at the specified index
   std::string label(const std::size_t& index)const;

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

@@ -88,7 +88,7 @@ double Axis::getValue(const std::size_t& index, const std::size_t& verticalIndex
 specid_t Axis::spectraNo(const std::size_t& index) const
 {
   UNUSED_ARG(index)
-  throw std::domain_error("Cannot call spectraNo() on a non-spectra axis.");
+      throw std::domain_error("Cannot call spectraNo() on a non-spectra axis.");
 }
 
 } // namespace API

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

@@ -1178,6 +1178,26 @@ void IFunction::storeAttributeValue(const std::string& name, const API::IFunctio
   }
 }
 
+/**
+ * Set the covariance matrix. Algorithm Fit sets this matrix to the top-level function
+ * after fitting. If the function is composite the matrix isn't set to its members.
+ * The matrix must be square and its size equal to the number of parameters of this function.
+ * @param covar :: A matrix to set.
+ */
+void IFunction::setCovarianceMatrix(boost::shared_ptr<Kernel::Matrix<double>> covar)
+{
+  // the matrix shouldn't be empty
+  if (!covar)
+  {
+    throw std::invalid_argument("IFunction: Cannot set an empty covariance matrix");
+  }
+  // the matrix should relate to this function
+  if (covar->numRows() != nParams() || covar->numCols() != nParams())
+  {
+    throw std::invalid_argument("IFunction: Covariance matrix has a wrong size");
+  }
+  m_covar = covar;
+}
 
 } // namespace API
 } // namespace Mantid

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

@@ -1416,34 +1416,35 @@ namespace Mantid
      */
     signal_t MatrixWorkspace::getSignalAtCoord(const coord_t * coords, const Mantid::API::MDNormalization & normalization) const
     {
+      if (this->axes() != 2)
+        throw std::invalid_argument("MatrixWorkspace::getSignalAtCoord() - Workspace can only have 2 axes, found " +\
+                                    boost::lexical_cast<std::string>(this->axes()));
+
       coord_t x = coords[0];
       coord_t y = coords[1];
-
       // First, find the workspace index
-      NumericAxis * ax1 = dynamic_cast<NumericAxis*>(this->getAxis(1));
+      Axis * ax1 = this->getAxis(1);
+      size_t wi(-1);
+      try
+      {
+        wi = ax1->indexOfValue(y);
+      }
+      catch(std::out_of_range &)
+      {
+        return std::numeric_limits<double>::quiet_NaN();
+      }
 
-      // If a spectra/text axis, just use the Y coord as the workspace index
-      size_t wi = size_t(y);
-      double yBinSize = 1.0;
-      if (ax1)
+      const auto & yVals = this->readY(wi);
+      double yBinSize(1.0); // only applies for volume normalization & numeric axis
+      if (normalization == VolumeNormalization && ax1->isNumeric())
       {
-        const MantidVec & yVals = ax1->getValues();
-        MantidVec::const_iterator it = std::lower_bound(yVals.begin(), yVals.end(), y);
-        if (it == yVals.end())
+        if (wi + 1 == this->getNumberHistograms() && this->getNumberHistograms() > 1)
         {
-          // Out of range
-          return std::numeric_limits<double>::quiet_NaN();
+          yBinSize =  yVals[wi] - yVals[wi-1];
         }
-        // The workspace index is the point in the vector that we found
-        wi = it - yVals.begin();
-
-        // Find the size of the bin in Y, if needed
-        if (normalization == VolumeNormalization)
+        else
         {
-          if ((it+1) == yVals.end() && (yVals.size() > 1))
-            yBinSize = *it - *(it-1);
-          else
-            yBinSize = *(it+1) - *it;
+          yBinSize = yVals[wi+1] - yVals[wi];
         }
       }
 
@@ -1461,7 +1462,7 @@ namespace Mantid
           size_t i = (it - X.begin());
           if (i > 0)
           {
-            double y = this->readY(wi)[i-1];
+            double y = yVals[i-1];
             // What is our normalization factor?
             switch (normalization)
             {
@@ -1487,9 +1488,6 @@ namespace Mantid
     }
 
 
-
-
-
     //--------------------------------------------------------------------------------------------
     /** Save the spectra detector map to an open NeXus file.
      * @param file :: open NeXus file