Merge branch 'master' into bugfix/10345_coverity_issues_in_mantidqt

Conflicts:
	Code/Mantid/MantidQt/CustomInterfaces/src/JumpFit.cpp
	Code/Mantid/MantidQt/SpectrumViewer/src/SpectrumView.cpp

Refs #10345

Code/Mantid/Build/CMake/DarwinSetup.cmake

@@ -84,6 +84,7 @@ set ( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64 -std=c++0x" )
 set ( CMAKE_XCODE_ATTRIBUTE_CLANG_CXX_LANGUAGE_STANDARD "c++0x" )
 
 if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+  set ( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++" )
   set ( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated-register" )
   set ( CMAKE_XCODE_ATTRIBUTE_OTHER_CPLUSPLUSFLAGS "-Wno-deprecated-register")
   set ( CMAKE_XCODE_ATTRIBUTE_CLANG_CXX_LIBRARY "libc++" )
@@ -120,8 +121,14 @@ if (OSX_VERSION VERSION_LESS 10.9)
  set ( SITEPACKAGES /Library/Python/${PY_VER}/site-packages )
 else()
  # Assume we are using homebrew for now
+ # set Deployment target to 10.8
+ set ( CMAKE_OSX_SYSROOT /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk )
+ set ( CMAKE_OSX_ARCHITECTURES x86_64 )
+ set ( CMAKE_OSX_DEPLOYMENT_TARGET 10.8 )
  set ( PYQT4_PYTHONPATH /usr/local/lib/python${PY_VER}/site-packages/PyQt4 )
  set ( SITEPACKAGES /usr/local/lib/python${PY_VER}/site-packages )
+ # use homebrew OpenSSL package
+ set ( OPENSSL_ROOT_DIR /usr/local/opt/openssl )
 endif()
 
 # Python packages

Code/Mantid/Build/CMake/FindPyQt.py

@@ -1,25 +1,48 @@
 # Copyright (c) 2007, Simon Edwards <simon@simonzone.com>
+# Copyright (c) 2014, Raphael Kubo da Costa <rakuco@FreeBSD.org>
 # Redistribution and use is allowed according to the terms of the BSD license.
 # For details see the accompanying COPYING-CMAKE-SCRIPTS file.
 
-import PyQt4.pyqtconfig
+import PyQt4.QtCore
+import os
+import sys
 
-pyqtcfg = PyQt4.pyqtconfig.Configuration()
-print("pyqt_version:%06.0x" % pyqtcfg.pyqt_version)
-print("pyqt_version_str:%s" % pyqtcfg.pyqt_version_str)
-
-pyqt_version_tag = ""
-in_t = False
-for item in pyqtcfg.pyqt_sip_flags.split(' '):
-    if item=="-t":
-        in_t = True
-    elif in_t:
-        if item.startswith("Qt_4"):
-            pyqt_version_tag = item
+def get_default_sip_dir():
+    # This is based on QScintilla's configure.py, and only works for the
+    # default case where installation paths have not been changed in PyQt's
+    # configuration process.
+    if sys.platform == 'win32':
+        pyqt_sip_dir = os.path.join(sys.platform, 'sip', 'PyQt4')
     else:
-        in_t = False
-print("pyqt_version_tag:%s" % pyqt_version_tag)
+        pyqt_sip_dir = os.path.join(sys.platform, 'share', 'sip', 'PyQt4')
+    return pyqt_sip_dir
+
+def get_qt4_tag(sip_flags):
+    in_t = False
+    for item in sip_flags.split(' '):
+        if item == '-t':
+            in_t = True
+        elif in_t:
+            if item.startswith('Qt_4'):
+                return item
+        else:
+            in_t = False
+    raise ValueError('Cannot find Qt\'s tag in PyQt4\'s SIP flags.')
 
-print("pyqt_sip_dir:%s" % pyqtcfg.pyqt_sip_dir)
-print("pyqt_sip_flags:%s" % pyqtcfg.pyqt_sip_flags)
+if __name__ == '__main__':
+    try:
+        import PyQt4.pyqtconfig
+        pyqtcfg = PyQt4.pyqtconfig.Configuration()
+        sip_dir = pyqtcfg.pyqt_sip_dir
+        sip_flags = pyqtcfg.pyqt_sip_flags
+    except ImportError:
+        # PyQt4 >= 4.10.0 was built with configure-ng.py instead of
+        # configure.py, so pyqtconfig.py is not installed.
+        sip_dir = get_default_sip_dir()
+        sip_flags = PyQt4.QtCore.PYQT_CONFIGURATION['sip_flags']
 
+    print('pyqt_version:%06.x' % PyQt4.QtCore.PYQT_VERSION)
+    print('pyqt_version_str:%s' % PyQt4.QtCore.PYQT_VERSION_STR)
+    print('pyqt_version_tag:%s' % get_qt4_tag(sip_flags))
+    print('pyqt_sip_dir:%s' % sip_dir)
+    print('pyqt_sip_flags:%s' % sip_flags)

Code/Mantid/Build/CMake/FindPyQt4.cmake

@@ -9,16 +9,20 @@
 # Find the installed version of PyQt4. FindPyQt4 should only be called after
 # Python has been found.
 #
-# This file defines the following variables:
+# This file defines the following variables, which can also be overriden by
+# users:
 #
 # PYQT4_VERSION - The version of PyQt4 found expressed as a 6 digit hex number
-#     suitable for comparision as a string
+#     suitable for comparison as a string
 #
 # PYQT4_VERSION_STR - The version of PyQt4 as a human readable string.
 #
-# PYQT4_VERSION_TAG - The PyQt version tag using by PyQt's sip files.
+# PYQT4_VERSION_TAG - The Qt4 version tag used by PyQt's sip files.
 #
-# PYQT4_SIP_DIR - The directory holding the PyQt4 .sip files.
+# PYQT4_SIP_DIR - The directory holding the PyQt4 .sip files. This can be unset
+# if PyQt4 was built using its new build system and pyqtconfig.py is not
+# present on the system, as in this case its value cannot be determined
+# automatically.
 #
 # PYQT4_SIP_FLAGS - The SIP flags used to build PyQt.
 
@@ -30,19 +34,38 @@ ELSE(EXISTS PYQT4_VERSION)
   FIND_FILE(_find_pyqt_py FindPyQt.py PATHS ${CMAKE_MODULE_PATH})
 
   EXECUTE_PROCESS(COMMAND ${PYTHON_EXECUTABLE} ${_find_pyqt_py} OUTPUT_VARIABLE pyqt_config)
-  IF( NOT ${pyqt_config} MATCHES "Traceback" )
-    STRING(REGEX REPLACE "^pyqt_version:([^\n]+).*$" "\\1" PYQT4_VERSION ${pyqt_config})
-    STRING(REGEX REPLACE ".*\npyqt_version_str:([^\n]+).*$" "\\1" PYQT4_VERSION_STR ${pyqt_config})
-    STRING(REGEX REPLACE ".*\npyqt_version_tag:([^\n]+).*$" "\\1" PYQT4_VERSION_TAG ${pyqt_config})
-    STRING(REGEX REPLACE ".*\npyqt_sip_dir:([^\n]+).*$" "\\1" PYQT4_SIP_DIR ${pyqt_config})
-    STRING(REGEX REPLACE ".*\npyqt_sip_flags:([^\n]+).*$" "\\1" PYQT4_SIP_FLAGS ${pyqt_config})
+  IF(pyqt_config)
+    STRING(REGEX MATCH "^pyqt_version:([^\n]+).*$" _dummy ${pyqt_config})
+    SET(PYQT4_VERSION "${CMAKE_MATCH_1}" CACHE STRING "PyQt4's version as a 6-digit hexadecimal number")
 
-    SET(PYQT4_FOUND TRUE)
-  ENDIF()
+    STRING(REGEX MATCH ".*\npyqt_version_str:([^\n]+).*$" _dummy ${pyqt_config})
+    SET(PYQT4_VERSION_STR "${CMAKE_MATCH_1}" CACHE STRING "PyQt4's version as a human-readable string")
 
-  include ( FindPackageHandleStandardArgs )
-  find_package_handle_standard_args ( PyQt4 DEFAULT_MSG PYQT4_VERSION )
+    STRING(REGEX MATCH ".*\npyqt_version_tag:([^\n]+).*$" _dummy ${pyqt_config})
+    SET(PYQT4_VERSION_TAG "${CMAKE_MATCH_1}" CACHE STRING "The Qt4 version tag used by PyQt4's .sip files")
 
-  mark_as_advanced ( _find_pyqt_py )
+    STRING(REGEX MATCH ".*\npyqt_sip_dir:([^\n]+).*$" _dummy ${pyqt_config})
+    SET(PYQT4_SIP_DIR "${CMAKE_MATCH_1}" CACHE FILEPATH "The base directory where PyQt4's .sip files are installed")
+
+    STRING(REGEX MATCH ".*\npyqt_sip_flags:([^\n]+).*$" _dummy ${pyqt_config})
+    SET(PYQT4_SIP_FLAGS "${CMAKE_MATCH_1}" CACHE STRING "The SIP flags used to build PyQt4")
+
+    IF(NOT IS_DIRECTORY "${PYQT4_SIP_DIR}")
+      MESSAGE(WARNING "The base directory where PyQt4's SIP files are installed could not be determined. This usually means PyQt4 was built with its new build system and pyqtconfig.py is not present.\n"
+                      "Please set the PYQT4_SIP_DIR variable manually.")
+    ELSE(NOT IS_DIRECTORY "${PYQT4_SIP_DIR}")
+      SET(PYQT4_FOUND TRUE)
+    ENDIF(NOT IS_DIRECTORY "${PYQT4_SIP_DIR}")
+  ENDIF(pyqt_config)
+
+  IF(PYQT4_FOUND)
+    IF(NOT PYQT4_FIND_QUIETLY)
+      MESSAGE(STATUS "Found PyQt4 version: ${PYQT4_VERSION_STR}")
+    ENDIF(NOT PYQT4_FIND_QUIETLY)
+  ELSE(PYQT4_FOUND)
+    IF(PYQT4_FIND_REQUIRED)
+      MESSAGE(FATAL_ERROR "Could not find Python")
+    ENDIF(PYQT4_FIND_REQUIRED)
+  ENDIF(PYQT4_FOUND)
 
 ENDIF(EXISTS PYQT4_VERSION)

Code/Mantid/Build/CMake/GNUSetup.cmake

@@ -6,16 +6,12 @@
 # project settings should be included in the relevant CMakeLists.txt file
 # for that project.
 
-# Get the GCC version
-EXEC_PROGRAM(${CMAKE_CXX_COMPILER} ARGS --version | cut -d \" \" -f 3 OUTPUT_VARIABLE _compiler_output)
-STRING(REGEX REPLACE ".*([0-9]\\.[0-9]\\.[0-9]).*" "\\1" GCC_COMPILER_VERSION ${_compiler_output})
-MESSAGE(STATUS "gcc version: ${GCC_COMPILER_VERSION}")
-
-# Export the GCC compiler version globally
-set(GCC_COMPILER_VERSION ${GCC_COMPILER_VERSION} CACHE INTERNAL "")
+# Set our own compiler version flag from the cmake one and export it globally
+set( GCC_COMPILER_VERSION ${CMAKE_CXX_COMPILER_VERSION} CACHE INTERNAL "")
+message( STATUS "gcc version: ${GCC_COMPILER_VERSION}" )
 
 # Global warning flags.
-set( GNUFLAGS "-Wall -Wextra -Wconversion -Winit-self -Wpointer-arith -Wcast-qual -Wcast-align -fno-common" ) 
+set( GNUFLAGS "-Wall -Wextra -Wconversion -Winit-self -Wpointer-arith -Wcast-qual -Wcast-align -fno-common" )
 # Disable some warnings about deprecated headers and type conversions that
 # we can't do anything about
 # -Wno-deprecated: Do not warn about use of deprecated headers.
@@ -38,4 +34,3 @@ set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${GNUFLAGS}" )
 set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${GNUFLAGS} -Woverloaded-virtual -fno-operator-names -std=c++0x" )
 # Cleanup
 set ( GNUFLAGS )
-

Code/Mantid/Build/class_maker.py

@@ -129,6 +129,8 @@ def write_source(subproject, classname, filename, args):
     algorithm_source = """
   //----------------------------------------------------------------------------------------------
 
+  /// Algorithms name for identification. @see Algorithm::name
+  const std::string %s::name() const { return "%s"; }
 
   /// Algorithm's version for identification. @see Algorithm::version
   int %s::version() const { return 1;};
@@ -156,7 +158,7 @@ def write_source(subproject, classname, filename, args):
     // TODO Auto-generated execute stub
   }
 
-""" % (classname, classname, classname, classname, classname)
+""" % (classname, classname, classname, classname, classname, classname, classname)
 
     if not args.alg:
         algorithm_top = ""

Code/Mantid/CMakeLists.txt

@@ -121,6 +121,7 @@ set ( CORE_MANTIDLIBS Kernel Geometry API )
 
 # Add a target for all GUI tests
 add_custom_target ( GUITests )
+add_dependencies ( GUITests MantidWidgetsTest)
 add_dependencies ( check GUITests )
 # Collect all tests together
 add_custom_target ( AllTests )

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

@@ -71,6 +71,7 @@ class IMDNode
     *@param loadFileData -- if true, the data on HDD and not yet in memory are loaded into memory before deleting fileBacked information, 
                             if false, all on HDD contents are discarded, which can break the data integrity (used by destructor)  */
     virtual void clearFileBacked(bool loadFileData)=0;
+    virtual void reserveMemoryForLoad(uint64_t)=0;
 
     /**Save the box at specific disk position using the class, respoinsible for the file IO. */
     virtual void saveAt(API::IBoxControllerIO *const /*saver */,  uint64_t /*position*/)const=0;

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

@@ -16,6 +16,7 @@
 #include "MantidAPI/Run.h"
 #include "MantidAPI/Sample.h"
 #include "MantidAPI/SpectraDetectorTypes.h"
+#include "MantidKernel/EmptyValues.h"
 
 
 namespace Mantid
@@ -33,6 +34,13 @@ namespace Mantid
   {
     class SpectrumDetectorMapping;
 
+    /// typedef for the image type
+    typedef std::vector<std::vector<double>> MantidImage;
+    /// shared pointer to MantidImage
+    typedef boost::shared_ptr<MantidImage> MantidImage_sptr;
+    /// shared pointer to const MantidImage
+    typedef boost::shared_ptr<const MantidImage> MantidImage_const_sptr;
+
     //----------------------------------------------------------------------
     /** Base MatrixWorkspace Abstract Class.
 
@@ -227,6 +235,9 @@ namespace Mantid
       /// Return a vector with the integrated counts for all spectra withing the given range
       virtual void getIntegratedSpectra(std::vector<double> & out, const double minX, const double maxX, const bool entireRange) const;
 
+      /// Return an index in the X vector for an x-value close to a given value
+      std::pair<size_t,double> getXIndex(size_t i, double x, bool isLeft = true, size_t start = 0) const;
+
       //----------------------------------------------------------------------
 
       int axes() const;
@@ -311,6 +322,25 @@ namespace Mantid
       // End IMDWorkspace methods
       //=====================================================================================
 
+      //=====================================================================================
+      // Image methods
+      //=====================================================================================
+
+      /// Get start and end x indices for images
+      std::pair<size_t,size_t> getImageStartEndXIndices( size_t i, double startX, double endX ) const;
+      /// Create an image of Ys.
+      MantidImage_sptr getImageY (size_t start = 0, size_t stop = 0, size_t width = 0, double startX = EMPTY_DBL(), double endX = EMPTY_DBL() ) const;
+      /// Create an image of Es.
+      MantidImage_sptr getImageE (size_t start = 0, size_t stop = 0, size_t width = 0, double startX = EMPTY_DBL(), double endX = EMPTY_DBL() ) const;
+      /// Copy the data (Y's) from an image to this workspace.
+      void setImageY( const MantidImage &image, size_t start = 0 );
+      /// Copy the data from an image to this workspace's errors.
+      void setImageE( const MantidImage &image, size_t start = 0 );
+
+      //=====================================================================================
+      // End image methods
+      //=====================================================================================
+
     protected:
       MatrixWorkspace(Mantid::Geometry::INearestNeighboursFactory* factory = NULL);
 
@@ -328,6 +358,10 @@ namespace Mantid
       MatrixWorkspace(const MatrixWorkspace&);
       /// Private copy assignment operator. NO ASSIGNMENT ALLOWED
       MatrixWorkspace& operator=(const MatrixWorkspace&);
+      /// Create an MantidImage instance.
+      MantidImage_sptr getImage(const MantidVec& (MatrixWorkspace::*read)(std::size_t const) const, size_t start, size_t stop, size_t width, size_t indexStart, size_t indexEnd) const;
+      /// Copy data from an image.
+      void setImage( MantidVec& (MatrixWorkspace::*dataVec)(const std::size_t), const MantidImage &image, size_t start );
 
       /// Has this workspace been initialised?
       bool m_isInitialized;

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

@@ -10,12 +10,6 @@
 #include <string>
 #include <vector>
 
-#ifndef HAS_UNORDERED_MAP_H
-#include <map>
-#else
-#include <tr1/unordered_map>
-#endif
-
 namespace Mantid
 {
 namespace API

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

@@ -5,9 +5,8 @@
 // Includes
 //------------------------------------------------------------------------------
 #include "MantidAPI/DllConfig.h"
-#include "MantidKernel/V3D.h"
-#include "MantidKernel/Material.h"
 #include "MantidGeometry/Objects/Object.h"
+#include "MantidKernel/V3D.h"
 #include <vector>
 
 
@@ -28,28 +27,28 @@ namespace Mantid
     //------------------------------------------------------------------------------
     class SampleEnvironment;
 
-    /** 
-      This class stores information about the sample used in particular 
+    /**
+      This class stores information about the sample used in particular
       run. It is a type of ObjComponent meaning it has a shape, a position
       and a material.
 
       Copyright &copy; 2007-2012 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>
     */
@@ -82,10 +81,8 @@ namespace Mantid
 
       /** @name Material properties.*/
       //@{
-      /// Return the material
+      /// Return the material (convenience method)
       const Kernel::Material & getMaterial() const;
-      /// Set the type of material that this sample is composed from
-      void setMaterial(const Kernel::Material& material);
       //@}
 
       /** @name Access the environment information */
@@ -102,7 +99,7 @@ namespace Mantid
       const Geometry::OrientedLattice & getOrientedLattice() const;
       /// Get a reference to the sample's OrientedLattice
       Geometry::OrientedLattice & getOrientedLattice();
-      /** Set the pointer to OrientedLattice defining the sample's lattice and orientation. 
+      /** Set the pointer to OrientedLattice defining the sample's lattice and orientation.
           No copying is done in the class, but the class deletes pointer on destruction so the application, providing the pointer should not do it*/
       void setOrientedLattice(Geometry::OrientedLattice * latt);
       bool hasOrientedLattice() const;
@@ -129,18 +126,16 @@ namespace Mantid
       /// Sets the width
       void setWidth(double width);
       /// Returns the width
-      double getWidth() const;  
+      double getWidth() const;
       //@}
       /// Delete the oriented lattice
       void clearOrientedLattice();
 
-    private: 
+    private:
       /// The sample name
       std::string m_name;
       /// The sample shape object
       Geometry::Object m_shape;
-      /// The sample composition
-      Kernel::Material m_material;
       /// An owned pointer to the SampleEnvironment object
       boost::shared_ptr<SampleEnvironment> m_environment;
       /// Pointer to the OrientedLattice of the sample, NULL if not set.