Merge branch 'master' of https://github.com/mantidproject/mantid

Code/Mantid/Build/CMake/CommonSetup.cmake

@@ -70,6 +70,7 @@ set ( CMAKE_INCLUDE_PATH ${MAIN_CMAKE_INCLUDE_PATH} )
 
 ###########################################################################
 # Look for Git. Used for version headers - faked if not found.
+# Also makes sure our commit hooks are linked in the right place.
 ###########################################################################
 
 set ( MtdVersion_WC_LAST_CHANGED_REV 0 )
@@ -85,6 +86,7 @@ if ( GIT_FOUND )
                     WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
   )
   if ( NOT NOT_GIT_REPO ) # i.e This is a git repository!
+
     # Remove the tag name part
     string ( REGEX MATCH "[-](.*)" MtdVersion_WC_LAST_CHANGED_REV ${GIT_DESCRIBE} )
     # Extract the SHA1 part (with a 'g' prefix which stands for 'git')
@@ -97,7 +99,33 @@ if ( GIT_FOUND )
                       WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
     )
     string ( SUBSTRING ${MtdVersion_WC_LAST_CHANGED_DATE} 0 16 MtdVersion_WC_LAST_CHANGED_DATE )
+
+    ###########################################################################
+    # This part puts our hooks (in .githooks) into .git/hooks
+    ###########################################################################
+    # First need to find the top-level directory of the git repository
+    execute_process ( COMMAND ${GIT_EXECUTABLE} rev-parse --show-toplevel
+                      OUTPUT_VARIABLE GIT_TOP_LEVEL
+                      WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+    )
+    # N.B. The variable comes back from 'git describe' with a line feed on the end, so we need to lose that
+    string ( REGEX MATCH "(.*)[^\n]" GIT_TOP_LEVEL ${GIT_TOP_LEVEL} )
+    # Prefer symlinks on platforms that support it so we don't rely on cmake running to be up-to-date
+    # On Windows, we have to copy the file
+    if ( WIN32 )
+      execute_process ( COMMAND ${CMAKE_COMMAND} -E copy_if_different ${GIT_TOP_LEVEL}/.githooks/pre-commit
+                                                                      ${GIT_TOP_LEVEL}/.git/hooks )
+      execute_process ( COMMAND ${CMAKE_COMMAND} -E copy_if_different ${GIT_TOP_LEVEL}/.githooks/commit-msg
+                                                                      ${GIT_TOP_LEVEL}/.git/hooks )
+    else ()
+      execute_process ( COMMAND ${CMAKE_COMMAND} -E create_symlink ${GIT_TOP_LEVEL}/.githooks/pre-commit
+                                                                   ${GIT_TOP_LEVEL}/.git/hooks/pre-commit )
+      execute_process ( COMMAND ${CMAKE_COMMAND} -E create_symlink ${GIT_TOP_LEVEL}/.githooks/commit-msg
+                                                                   ${GIT_TOP_LEVEL}/.git/hooks/commit-msg )
+    endif ()
+
   endif()
+
 else()
   # Just use a dummy version number and print a warning
   message ( STATUS "Git not found - using dummy revision number and date" )

Code/Mantid/Build/class_maker.py

@@ -150,6 +150,7 @@ def write_source(subproject, classname, filename, args):
     if not args.alg:
         algorithm_top = ""
         algorithm_source = ""
+        s = ""
     else:
         s = """/*WIKI*
 TODO: Enter a full wiki-markup description of your algorithm here. You can then use the Build/wiki_maker.py script to generate your full wiki page.

Code/Mantid/Framework/API/CMakeLists.txt

@@ -9,6 +9,7 @@ set ( SRC_FILES
 	src/AnalysisDataService.cpp
 	src/ArchiveSearchFactory.cpp
 	src/Axis.cpp
+	src/BoxController.cpp
 	src/CatalogFactory.cpp
 	src/CloneableAlgorithm.cpp
 	src/Column.cpp
@@ -99,6 +100,7 @@ set ( INC_FILES
 	inc/MantidAPI/AnalysisDataService.h
 	inc/MantidAPI/ArchiveSearchFactory.h
 	inc/MantidAPI/Axis.h
+	inc/MantidAPI/BoxController.h
 	inc/MantidAPI/CatalogFactory.h
 	inc/MantidAPI/CloneableAlgorithm.h
 	inc/MantidAPI/Column.h
@@ -199,6 +201,7 @@ set ( TEST_FILES
 	test/AlgorithmTest.h
 	test/AnalysisDataServiceTest.h
 	test/AsynchronousTest.h
+	test/BoxControllerTest.h
 	test/CompositeFunctionTest.h
 	test/CoordTransformTest.h
 	test/CostFunctionFactoryTest.h

Code/Mantid/Framework/MDEvents/inc/MantidMDEvents/BoxController.h → Code/Mantid/Framework/API/inc/MantidAPI/BoxController.h

@@ -11,7 +11,7 @@
 
 namespace Mantid
 {
-namespace MDEvents
+namespace API
 {
 
 
@@ -492,7 +492,10 @@ namespace MDEvents
   /// Shared ptr to BoxController
   typedef boost::shared_ptr<BoxController> BoxController_sptr;
 
-}//namespace MDEvents
+  /// Shared ptr to a const BoxController
+  typedef boost::shared_ptr<const BoxController> BoxController_const_sptr;
+
+}//namespace API
 
 }//namespace Mantid
 

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

@@ -1,6 +1,7 @@
 #ifndef IMDEVENTWORKSPACE_H_
 #define IMDEVENTWORKSPACE_H_
 
+#include "MantidAPI/BoxController.h"
 #include "MantidAPI/DllConfig.h"
 #include "MantidAPI/ExperimentInfo.h"
 #include "MantidAPI/IMDWorkspace.h"
@@ -10,8 +11,8 @@
 #include "MantidGeometry/MDGeometry/MDDimensionExtents.h"
 #include "MantidGeometry/MDGeometry/MDHistoDimension.h"
 #include "MantidKernel/ProgressBase.h"
-#include <boost/shared_ptr.hpp>
 #include "MantidKernel/ThreadScheduler.h"
+#include <boost/shared_ptr.hpp>
 
 namespace Mantid
 {
@@ -42,6 +43,9 @@ namespace API
     /// Returns some information about the box controller, to be displayed in the GUI, for example
     virtual std::vector<std::string> getBoxControllerStats() const = 0;
 
+    virtual Mantid::API::BoxController_sptr getBoxController() = 0;
+    virtual Mantid::API::BoxController_const_sptr getBoxController() const = 0;
+
     /// Helper method that makes a table workspace with some box data
     virtual Mantid::API::ITableWorkspace_sptr makeBoxTable(size_t start, size_t num) = 0;
 

Code/Mantid/Framework/MDEvents/src/BoxController.cpp → Code/Mantid/Framework/API/src/BoxController.cpp

@@ -1,7 +1,7 @@
 #include "MantidKernel/Strings.h"
 #include "MantidKernel/System.h"
 #include "MantidKernel/VectorHelper.h"
-#include "MantidMDEvents/BoxController.h"
+#include "MantidAPI/BoxController.h"
 #include <boost/algorithm/string.hpp>
 #include <boost/format.hpp>
 #include <Poco/DOM/Attr.h>
@@ -20,7 +20,7 @@ using Mantid::Kernel::VectorHelper::splitStringIntoVector;
 
 namespace Mantid
 {
-namespace MDEvents
+namespace API
 {
 
   //-----------------------------------------------------------------------------------
@@ -158,7 +158,7 @@ namespace MDEvents
 
 } // namespace Mantid
 
-} // namespace MDEvents
+} // namespace API
 
 
 

Code/Mantid/Framework/MDEvents/test/BoxControllerTest.h → Code/Mantid/Framework/API/test/BoxControllerTest.h

@@ -2,14 +2,14 @@
 #define BOXPLITCONTROLLER_TEST_H
 
 #include "MantidKernel/DiskMRU.h"
-#include "MantidMDEvents/BoxController.h"
+#include "MantidAPI/BoxController.h"
 #include <cxxtest/TestSuite.h>
 #include <map>
 #include <memory>
 
 using namespace Mantid;
+using namespace Mantid::API;
 using namespace Mantid::Kernel;
-using namespace Mantid::MDEvents;
 
 class BoxControllerTest :    public CxxTest::TestSuite
 {

Code/Mantid/Framework/DataHandling/src/LoadEventNexus.cpp

@@ -749,6 +749,9 @@ void LoadEventNexus::init()
   setPropertyGroup("FilterMonByTimeStart", grp4);
   setPropertyGroup("FilterMonByTimeStop", grp4);
 
+  declareProperty(
+      new PropertyWithValue<bool>("MetaDataOnly", false, Direction::Input),
+      "If true, only the meta data and sample logs will be loaded.");
 }
 
 
@@ -917,6 +920,8 @@ void LoadEventNexus::makeMapToEventLists()
  */
 void LoadEventNexus::loadEvents(API::Progress * const prog, const bool monitors)
 {
+  bool metaDataOnly = getProperty("MetaDataOnly");
+
   // Get the time filters
   setTimeFilters(monitors);
 
@@ -967,6 +972,26 @@ void LoadEventNexus::loadEvents(API::Progress * const prog, const bool monitors)
   file.closeGroup();
   file.close();
 
+  // Delete the output workspace name if it existed
+  std::string outName = getPropertyValue("OutputWorkspace");
+  if (AnalysisDataService::Instance().doesExist(outName))
+    AnalysisDataService::Instance().remove( outName );
+
+  // set more properties on the workspace
+  loadEntryMetadata(m_filename, WS, m_top_entry_name);
+
+  if(metaDataOnly) {
+    //Now, create a default X-vector for histogramming, with just 2 bins.
+    Kernel::cow_ptr<MantidVec> axis;
+    MantidVec& xRef = axis.access();
+    xRef.resize(2);
+    xRef[0] = static_cast<double>(std::numeric_limits<uint32_t>::max()) * 0.1 - 1; //Just to make sure the bins hold it all
+    xRef[1] = 1;
+    //Set the binning axis using this.
+    WS->setAllX(axis);
+    return;
+  }
+
   // --------- Loading only one bank ? ----------------------------------
   std::string onebank = getProperty("BankName");
   bool doOneBank = (onebank != "");
@@ -995,11 +1020,6 @@ void LoadEventNexus::loadEvents(API::Progress * const prog, const bool monitors)
     onebank = "";
   }
 
-  // Delete the output workspace name if it existed
-  std::string outName = getPropertyValue("OutputWorkspace");
-  if (AnalysisDataService::Instance().doesExist(outName))
-    AnalysisDataService::Instance().remove( outName );
-
   prog->report("Initializing all pixels");
 
   //----------------- Pad Empty Pixels -------------------------------
@@ -1097,9 +1117,6 @@ void LoadEventNexus::loadEvents(API::Progress * const prog, const bool monitors)
   //Set the binning axis using this.
   WS->setAllX(axis);
 
-  // set more properties on the workspace
-  loadEntryMetadata(m_filename, WS, m_top_entry_name);
-
   // if there is time_of_flight load it
   loadTimeOfFlight(m_filename, WS, m_top_entry_name,classType);
 }

Code/Mantid/Framework/DataHandling/src/LoadNexusProcessed.cpp

@@ -286,7 +286,7 @@ API::MatrixWorkspace_sptr LoadNexusProcessed::loadEventEntry(NXData & wksp_cls,
       el.reserve(index_end - index_start);
       el.clearDetectorIDs();
 
-      for (long i=index_start; i<index_end; i++)
+      for (int64_t i=index_start; i<index_end; i++)
       switch (type)
       {
       case TOF:
@@ -485,7 +485,7 @@ API::Workspace_sptr LoadNexusProcessed::loadEntry(NXRoot & root, const std::stri
     //// validate the optional spectrum parameters, if set
     checkOptionalProperties(nspectra);
     // Actual number of spectra in output workspace (if only a range was going to be loaded)
-    int total_specs=calculateWorkspacesize(nspectra);
+    size_t total_specs=calculateWorkspacesize(nspectra);
 
     //// Create the 2D workspace for the output
     local_workspace = boost::dynamic_pointer_cast<API::MatrixWorkspace>

Code/Mantid/Framework/MDAlgorithms/src/ConvertToQ3DdE.cpp

@@ -86,7 +86,7 @@ boost::shared_ptr<MDEvents::MDEventWorkspace<MDE,4> > create_empty4DEventWS(cons
       ws->initialize();
 
       // Build up the box controller
-      MDEvents::BoxController_sptr bc = ws->getBoxController();
+      Mantid::API::BoxController_sptr bc = ws->getBoxController();
       bc->setSplitInto(5);
 //      bc->setSplitThreshold(1500);
       bc->setSplitThreshold(10);

Code/Mantid/Framework/MDAlgorithms/src/ConvertToQNDany.cpp

@@ -92,7 +92,7 @@ boost::shared_ptr<MDEvents::MDEventWorkspace<MDEvents::MDEvent<nd>, nd> > create
       ws->initialize();
 
       // Build up the box controller
-      MDEvents::BoxController_sptr bc = ws->getBoxController();
+      Mantid::API::BoxController_sptr bc = ws->getBoxController();
       bc->setSplitInto(5);
 //      bc->setSplitThreshold(1500);
       bc->setSplitThreshold(10);

Code/Mantid/Framework/MDEvents/CMakeLists.txt

@@ -3,7 +3,7 @@ set ( SRC_FILES
 	src/AffineMatrixParameter.cpp
 	src/AffineMatrixParameterParser.cpp
 	src/BinToMDHistoWorkspace.cpp
-	src/BoxController.cpp
+	src/BoxControllerSettingsAlgorithm.cpp
 	src/CentroidPeaksMD.cpp
 	src/CloneMDWorkspace.cpp
 	src/ConvertToDiffractionMDWorkspace.cpp
@@ -50,7 +50,7 @@ set ( INC_FILES
 	inc/MantidMDEvents/AffineMatrixParameter.h
 	inc/MantidMDEvents/AffineMatrixParameterParser.h
 	inc/MantidMDEvents/BinToMDHistoWorkspace.h
-	inc/MantidMDEvents/BoxController.h
+	inc/MantidMDEvents/BoxControllerSettingsAlgorithm.h
 	inc/MantidMDEvents/CentroidPeaksMD.h
 	inc/MantidMDEvents/CloneMDWorkspace.h
 	inc/MantidMDEvents/ConvertToDiffractionMDWorkspace.h
@@ -89,7 +89,7 @@ set ( INC_FILES
 set ( TEST_FILES
 	test/AffineMatrixParameterParserTest.h
 	test/AffineMatrixParameterTest.h
-	test/BoxControllerTest.h
+	test/BoxControllerSettingsAlgorithmTest.h
 	test/CentroidPeaksMDTest.h
 	test/CloneMDWorkspaceTest.h
 	test/ConvertToDiffractionMDWorkspaceTest.h

Code/Mantid/Framework/MDEvents/inc/MantidMDEvents/BoxControllerSettingsAlgorithm.h

@@ -0,0 +1,63 @@
+#ifndef MANTID_MDEVENTS_BOXCONTROLLERSETTINGSALGORITHM_H_
+#define MANTID_MDEVENTS_BOXCONTROLLERSETTINGSALGORITHM_H_
+
+#include "MantidKernel/System.h"
+#include "MantidAPI/Algorithm.h" 
+#include "MantidAPI/BoxController.h"
+
+namespace Mantid
+{
+namespace MDEvents
+{
+
+  /** An abstract algorithm sub-class for algorithms that
+   * define properties for BoxController settings.
+   *
+   * This will be inherited by other algorithms as required.
+    
+    @author Janik Zikovsky
+    @date 2011-11-02
+
+    Copyright © 2011 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://svn.mantidproject.org/mantid/trunk/Code/Mantid>
+    Code Documentation is available at: <http://doxygen.mantidproject.org>
+  */
+  class DLLExport BoxControllerSettingsAlgorithm  : public API::Algorithm
+  {
+  public:
+    BoxControllerSettingsAlgorithm();
+    ~BoxControllerSettingsAlgorithm();
+
+  protected:
+    /// Initialise the properties
+    void initBoxControllerProps(const std::string & SplitInto="5", int SplitThreshold=1000, int MaxRecursionDepth=5);
+
+    /// Set the settings in the given box controller
+    void setBoxController(Mantid::API::BoxController_sptr bc);
+
+    std::string getBoxSettingsGroupName()
+    { return "Box Splitting Settings"; }
+
+  };
+
+
+} // namespace MDEvents
+} // namespace Mantid
+
+#endif  /* MANTID_MDEVENTS_BOXCONTROLLERSETTINGSALGORITHM_H_ */