Merge branch 'master' into 11350_converttomd_no_expt_info_loading

[skip ci]

Code/Mantid/Build/CMake/CommonSetup.cmake

@@ -41,7 +41,7 @@ set ( TESTING_TIMEOUT 300 CACHE INTEGER
       "Timeout in seconds for each test (default 300=5minutes)")
 
 ###########################################################################
-# Look for dependencies - bail out if any not found
+# Look for dependencies
 ###########################################################################
 
 set ( Boost_NO_BOOST_CMAKE TRUE )
@@ -71,6 +71,14 @@ set ( CMAKE_INCLUDE_PATH ${CMAKE_INCLUDE_PATH}/zlib123 )
 find_package ( ZLIB REQUIRED )
 set ( CMAKE_INCLUDE_PATH ${MAIN_CMAKE_INCLUDE_PATH} )
 
+if (${CMAKE_SYSTEM_NAME} MATCHES "Windows" OR OSX_VERSION VERSION_LESS 10.9)
+  set (HDF5_DIR "${CMAKE_MODULE_PATH}")
+  find_package ( HDF5 COMPONENTS HL REQUIRED
+    CONFIGS hdf5-config.cmake )
+else()
+  find_package ( HDF5 COMPONENTS HL REQUIRED )
+endif()
+
 find_package ( PythonInterp )
 
 if ( MSVC )

Code/Mantid/Build/CMake/FindOpenCascade.cmake

@@ -18,50 +18,61 @@ if ( WIN32 )
   add_definitions ( -DWNT )
 endif ( WIN32 )
 
-set ( OC_REDHAT_RPM /opt/OpenCASCADE/lib64 )
+find_path ( OPENCASCADE_LIBRARY_DIR libTKernel.so PATHS
+                /opt/OpenCASCADE/lib64
+                $ENV{CASROOT}/lib64
+                /opt/OpenCASCADE/lib
+                $ENV{CASROOT}/lib
+                /opt/OpenCASCADE/lib32
+                $ENV{CASROOT}/lib32
+)
+
 find_library ( OPENCASCADE_LIB_TKERNEL
                  NAMES TKernel
-                 PATHS ${OC_REDHAT_RPM}         
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 find_library ( OPENCASCADE_LIB_TKBO
                  NAMES TKBO
-                 PATHS ${OC_REDHAT_RPM}         
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 find_library ( OPENCASCADE_LIB_TKPRIM
                  NAMES TKPrim
-                 PATHS ${OC_REDHAT_RPM}         
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 find_library ( OPENCASCADE_LIB_TKMESH
                  NAMES TKMesh
-                 PATHS ${OC_REDHAT_RPM}         
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 find_library ( OPENCASCADE_LIB_TKBREP
                  NAMES TKBRep
-                 PATHS ${OC_REDHAT_RPM}         
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 find_library ( OPENCASCADE_LIB_TKTOPALGO
                  NAMES TKTopAlgo
-                 PATHS ${OC_REDHAT_RPM}         
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 find_library ( OPENCASCADE_LIB_TKMATH
                  NAMES TKMath
-                 PATHS ${OC_REDHAT_RPM}         
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 find_library ( OPENCASCADE_LIB_TKG2D
                  NAMES TKG2d
-                 PATHS ${OC_REDHAT_RPM}         
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 
 find_library ( OPENCASCADE_LIB_TKG3D
                  NAMES TKG3d
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 
 find_library ( OPENCASCADE_LIB_TKGEOMBASE
                  NAMES TKGeomBase
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 
 find_library ( OPENCASCADE_LIB_TKGEOMALGO
                  NAMES TKGeomAlgo
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 
 set ( OPENCASCADE_LIBRARIES
@@ -83,7 +94,7 @@ set ( OPENCASCADE_LIBRARIES
 include ( FindPackageHandleStandardArgs )
 find_package_handle_standard_args( OpenCascade DEFAULT_MSG OPENCASCADE_LIBRARIES OPENCASCADE_INCLUDE_DIR )
 
-mark_as_advanced ( OPENCASCADE_INCLUDE_DIR
+mark_as_advanced ( OPENCASCADE_INCLUDE_DIR OPENCASCADE_LIBRARY_DIR
                    OPENCASCADE_LIB_TKERNEL OPENCASCADE_LIB_TKBO 
                    OPENCASCADE_LIB_TKPRIM OPENCASCADE_LIB_TKMESH
                    OPENCASCADE_LIB_TKBREP OPENCASCADE_LIB_TKTOPALGO 

Code/Mantid/Build/CMake/FindQwt.cmake

@@ -9,7 +9,7 @@
 find_path ( QWT_INCLUDE_DIR qwt.h 
             PATHS /opt/include /usr/local/include /usr/include ${CMAKE_INCLUDE_PATH}
             PATH_SUFFIXES qwt5 qwt5-qt4 qwt-qt4 qwt )
-find_library ( QWT_LIBRARY NAMES qwt5-qt4 qwt-qt4 qwt )
+find_library ( QWT_LIBRARY NAMES qwt5-qt4 qwt-qt4 qwt5 qwt )
 find_library ( QWT_LIBRARY_DEBUG qwtd )
 
 # in REQUIRED mode: terminate if one of the above find commands failed

Code/Mantid/Build/CMake/LinuxPackageScripts.cmake

@@ -26,21 +26,6 @@ set ( CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/${LIB_DIR};${CMAKE_INSTALL_PRE
 # Required for Fedora >= 18 and RHEL >= 7
 set ( CPACK_RPM_EXCLUDE_FROM_AUTO_FILELIST_ADDITION /opt /usr/share/applications /usr/share/pixmaps )
 
-###########################################################################
-# LD_PRELOAD TCMalloc
-###########################################################################
-# User systems will only have the libraries and not the symbolic link
-# so we must set the preload to the versioned library. We will assume it is
-# in the same location as the system that the package was built on
-if ( TCMALLOC_LIBRARIES )
-  execute_process ( COMMAND readlink --no-newline --canonicalize-existing ${TCMALLOC_LIBRARIES}
-                    OUTPUT_VARIABLE TCMALLOC_PRELOAD
-                    RESULT_VARIABLE READLINK_RESULT )
-  if ( READLINK_RESULT EQUAL 1 )
-    message ( FATAL_ERROR "Unable to find real file that tcmalloc symlink, ${TCMALLOC_LIBRARIES}, points to." )
-  endif()
-endif()
-
 ###########################################################################
 # Environment scripts (profile.d)
 ###########################################################################
@@ -151,6 +136,12 @@ configure_file ( ${CMAKE_MODULE_PATH}/Packaging/launch_mantidplot.sh.in
 # Needs to be executable
 execute_process ( COMMAND "chmod" "+x" "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/launch_mantidplot.sh"
                   OUTPUT_QUIET ERROR_QUIET )
+configure_file ( ${CMAKE_MODULE_PATH}/Packaging/mantidpython.in 
+                 ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/mantidpython @ONLY )
+# Needs to be executable
+execute_process ( COMMAND "chmod" "+x" "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/mantidpython"
+                  OUTPUT_QUIET ERROR_QUIET )
+
 # Package version
 set ( MANTIDPLOT_EXEC MantidPlot_exe )
 configure_file ( ${CMAKE_MODULE_PATH}/Packaging/launch_mantidplot.sh.in 
@@ -161,3 +152,11 @@ install ( FILES ${CMAKE_CURRENT_BINARY_DIR}/launch_mantidplot.sh.install
           GROUP_EXECUTE GROUP_READ
           WORLD_EXECUTE WORLD_READ
 )
+configure_file ( ${CMAKE_MODULE_PATH}/Packaging/mantidpython.in 
+                 ${CMAKE_CURRENT_BINARY_DIR}/mantidpython.install @ONLY )
+install ( FILES ${CMAKE_CURRENT_BINARY_DIR}/mantidpython.install
+          DESTINATION ${BIN_DIR} RENAME mantidpython
+          PERMISSIONS OWNER_EXECUTE OWNER_WRITE OWNER_READ
+          GROUP_EXECUTE GROUP_READ
+          WORLD_EXECUTE WORLD_READ
+)

Code/Mantid/Build/CMake/Packaging/launch_mantidplot.sh.in

@@ -9,7 +9,7 @@ SCRIPTFILE=$(readlink -f "$0")
 INSTALLDIR=$(echo $SCRIPTFILE | sed -r -e 's|^(.*)/(.*)$|\1|g') #.* is greedy and eats up until the final slash
 
 # Define extra libraries and load paths
-LOCAL_PRELOAD=@TCMALLOC_PRELOAD@
+LOCAL_PRELOAD=`readlink --no-newline --canonicalize-existing @TCMALLOC_LIBRARIES@`
 if [ -n "${LD_PRELOAD}" ]; then
     LOCAL_PRELOAD=${LOCAL_PRELOAD}:${LD_PRELOAD}
 fi
@@ -21,4 +21,6 @@ else
 fi
 
 # Launch
-LD_PRELOAD=${LOCAL_PRELOAD} TCMALLOC_RELEASE_RATE=${TCM_RELEASE} LD_LIBRARY_PATH=${LOCAL_LDPATH} QT_API=pyqt @WRAPPER_PREFIX@$INSTALLDIR/@MANTIDPLOT_EXEC@ $*@WRAPPER_POSTFIX@
+LD_PRELOAD=${LOCAL_PRELOAD} TCMALLOC_RELEASE_RATE=${TCM_RELEASE} \
+    LD_LIBRARY_PATH=${LOCAL_LDPATH} QT_API=pyqt \
+    @WRAPPER_PREFIX@$INSTALLDIR/@MANTIDPLOT_EXEC@ $*@WRAPPER_POSTFIX@

Code/Mantid/Build/CMake/Packaging/mantidpython.in

@@ -0,0 +1,34 @@
+#!/bin/sh
+#
+# Launch Mantidplot using any necessary LD_PRELOAD or software collection behaviour
+#
+# Script is configured by CMake
+
+# Find out where we are
+SCRIPTFILE=$(readlink -f "$0")
+INSTALLDIR=$(echo $SCRIPTFILE | sed -r -e 's|^(.*)/(.*)$|\1|g') #.* is greedy and eats up until the final slash
+IPYTHON=$(command -v ipython)
+
+# Define extra libraries and load paths
+LOCAL_PRELOAD=`readlink --no-newline --canonicalize-existing @TCMALLOC_LIBRARIES@`
+if [ -n "${LD_PRELOAD}" ]; then
+    LOCAL_PRELOAD=${LOCAL_PRELOAD}:${LD_PRELOAD}
+fi
+LOCAL_LDPATH=@EXTRA_LDPATH@:${LD_LIBRARY_PATH}
+if [ -z "${TCMALLOC_RELEASE_RATE}" ]; then
+    TCM_RELEASE=10000
+else
+    TCM_RELEASE=${TCMALLOC_RELEASE_RATE}
+fi
+
+# Define extra libraries for python
+LOCAL_PYTHONPATH=@WRAPPER_PREFIX@$INSTALLDIR
+if [ -n "${PYTHONPATH}" ]; then
+    LOCAL_PYTHONPATH=${LOCAL_PYTHONPATH}:${PYTHONPATH}
+fi
+
+# Launch
+LD_PRELOAD=${LOCAL_PRELOAD} TCMALLOC_RELEASE_RATE=${TCM_RELEASE} \
+    LD_LIBRARY_PATH=${LOCAL_LDPATH} QT_API=pyqt \
+    PYTHONPATH=${LOCAL_PYTHONPATH} \
+    ${IPYTHON} $*@WRAPPER_POSTFIX@

Code/Mantid/Build/Jenkins/buildscript

@@ -85,6 +85,10 @@ else
   SCL_ON_RHEL6="eval"
 fi
 
+if [[ ${NODE_LABELS} == *rhel7* ]]; then
+  ON_RHEL7=true
+fi
+
 ###############################################################################
 # Check job requirements from the name
 ###############################################################################
@@ -212,6 +216,6 @@ fi
 # Run the system tests on RHEL6 when doing a pull request build. Run
 # from a package to have at least one Linux checks it install okay
 ###############################################################################
-if [[ "${ON_RHEL6}" == true ]] && [[ ${JOB_NAME} == *pull_requests* ]]; then
+if [[ "${ON_RHEL7}" == true ]] && [[ ${JOB_NAME} == *pull_requests* ]]; then
   $SCRIPT_DIR/systemtests
 fi

Code/Mantid/CMakeLists.txt

@@ -121,6 +121,7 @@ set( DOCS_BUILDDIR ${CMAKE_BINARY_DIR}/docs )
 # Framework Build options
 set ( CXXTEST_SINGLE_LOGFILE CACHE BOOL "Switch to have the tests for each package run together")
 set ( CXXTEST_ADD_PERFORMANCE OFF CACHE BOOL "Switch to add Performance tests to the list of tests run by ctest?")
+set ( ENABLE_OPENCASCADE ON CACHE BOOL "Enable OpenCascade-based 3D visualisation")
 
 add_subdirectory ( Framework )
 

Code/Mantid/Framework/API/inc/MantidAPI/FunctionDomain1D.h

@@ -52,6 +52,8 @@ class MANTID_API_DLL FunctionDomain1D : public FunctionDomain {
   double operator[](size_t i) const { return m_data[i]; }
   /// Get a pointer to i-th value
   const double *getPointerAt(size_t i) const { return m_data + i; }
+  /// Convert to a vector
+  std::vector<double> toVector() const;
 
 protected:
   /// Protected constructor, shouldn't be created directly. Use

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

@@ -103,6 +103,9 @@ class MANTID_API_DLL FunctionValues {
   /// instance.
   void setFitDataFromCalculated(const FunctionValues &values);
 
+  /// Return the calculated values as a vector
+  std::vector<double> toVector() const {return m_calculated;}
+
 protected:
   /// Copy calculated values to a buffer
   /// @param to :: Pointer to the buffer

Code/Mantid/Framework/API/src/FunctionDomain1D.cpp

@@ -7,6 +7,16 @@
 namespace Mantid {
 namespace API {
 
+/// Convert to a vector
+std::vector<double> FunctionDomain1D::toVector() const 
+{
+  std::vector<double> res;
+  if ( m_n > 0 ){
+    res.assign(m_data, m_data+m_n);
+  }
+  return res;
+}
+
 /**
   * Create a domain from a vector.
   * @param xvalues :: Vector with function arguments to be copied from.

Code/Mantid/Framework/CurveFitting/CMakeLists.txt

@@ -32,6 +32,7 @@ set ( SRC_FILES
 	src/DiffSphere.cpp
 	src/DynamicKuboToyabe.cpp
 	src/EndErfc.cpp
+	src/EstimatePeakErrors.cpp
 	src/ExpDecay.cpp
 	src/ExpDecayMuon.cpp
 	src/ExpDecayOsc.cpp
@@ -141,6 +142,7 @@ set ( INC_FILES
 	inc/MantidCurveFitting/DllConfig.h
 	inc/MantidCurveFitting/DynamicKuboToyabe.h
 	inc/MantidCurveFitting/EndErfc.h
+    inc/MantidCurveFitting/EstimatePeakErrors.h
 	inc/MantidCurveFitting/ExpDecay.h
 	inc/MantidCurveFitting/ExpDecayMuon.h
 	inc/MantidCurveFitting/ExpDecayOsc.h
@@ -245,6 +247,7 @@ set ( TEST_FILES
 	DiffSphereTest.h
 	DynamicKuboToyabeTest.h
 	EndErfcTest.h
+    EstimatePeakErrorsTest.h
 	ExpDecayMuonTest.h
 	ExpDecayOscTest.h
 	ExpDecayTest.h

Code/Mantid/Framework/CurveFitting/inc/MantidCurveFitting/EstimatePeakErrors.h

@@ -0,0 +1,50 @@
+#ifndef MANTID_CURVEFITTING_ESTIMATEPEAKERRORS_H_
+#define MANTID_CURVEFITTING_ESTIMATEPEAKERRORS_H_
+
+#include "MantidAPI/Algorithm.h"
+
+namespace Mantid {
+namespace CurveFitting {
+//---------------------------------------------------------------------------
+/**
+
+Copyright © 2013 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+National Laboratory & European Spallation Source
+
+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 EstimatePeakErrors : public API::Algorithm {
+public:
+  EstimatePeakErrors();
+
+  const std::string name() const;
+  virtual const std::string summary() const ;
+
+  int version() const;
+  const std::string category() const;
+
+private:
+  void init();
+  void exec();
+};
+
+} // namespace CurveFitting
+} // namespace Mantid
+
+#endif /* MANTID_CURVEFITTING_ESTIMATEPEAKERRORS_H_ */