Merge branch 'master' into feature/10470_grouped_dets_sxdnorm

Conflicts:
	Code/Mantid/Framework/MDAlgorithms/src/MDNormSXD.cpp
Refs #10470

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

@@ -1,5 +1,5 @@
 Name:           mantid-developer
-Version:        1.4
+Version:        1.5
 Release:        1%{?dist}
 Summary:        Meta Package to install dependencies for Mantid Development
 
@@ -19,6 +19,7 @@ Requires: git-all
 Requires: gsl-devel
 Requires: hdf-devel
 Requires: hdf5-devel
+Requires: jsoncpp-devel
 Requires: muParser-devel
 Requires: mxml-devel
 Requires: nexus >= 4.2

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

@@ -150,6 +150,8 @@ namespace Mantid
       virtual void saveNexus(::NeXus::File * file, const std::string & group,bool keepOpen=false) const;
       /// Load the run from a NeXus file with a given group name
       virtual void loadNexus(::NeXus::File * file, const std::string & group,bool keepOpen=false);
+      /// Clear the logs
+      void clearLogs();
 
     protected:
       /// A pointer to a property manager

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

@@ -369,44 +369,6 @@ class DLLExport IncreasingAxisValidator : public MatrixWorkspaceValidator
   }
 };
 
-//===============================================================================================
-/**
- * A validator which checks whether data in each spectrum of the input workspace are monotonically increasing.
- */
-class DLLExport IncreasingDataValidator : public MatrixWorkspaceValidator
-{
-public:
-  ///Gets the type of the validator
-  std::string getType() const { return "increasingdata"; }
-  /// Clone the current state
-  Kernel::IValidator_sptr clone() const { return boost::make_shared<IncreasingDataValidator>(*this); }
-
-private:
-  /** Validate a workspace.
-  *  @param value :: The workspace to test
-  *  @return A message for users with negative results, otherwise ""
-  */
-  std::string checkValidity( const MatrixWorkspace_sptr& value ) const
-  {
-    if ( value->blocksize() < 2 ) 
-    {
-      return "Spectra must have two or more data points (bins).";
-    }
-    for(size_t spec = 0; spec < value->getNumberHistograms(); ++spec)
-    {
-      auto &Y = value->readY( spec );
-      double y = Y.front();
-      for(auto it = Y.begin() + 1; it != Y.end(); ++it)
-      {
-        if ( y > *it ) return "Data in the workspace must monotonically increase.";
-        y = *it;
-      }
-    }
-    return "";
-  }
-
-};
-
 } // namespace API
 } // namespace Mantid
 

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

@@ -434,13 +434,22 @@ using namespace Kernel;
         if (prop)
         {
           if (m_manager.existsProperty(prop->name() ))
+          {
             m_manager.removeProperty(prop->name() );
+          }
           m_manager.declareProperty(prop);
         }
       }
     }
     if (!(group.empty()||keepOpen))file->closeGroup();
-
+  }
+
+  /**
+   * Clear the logs.
+   */
+  void LogManager::clearLogs()
+  {
+    m_manager.clear();
   }
 
   //-----------------------------------------------------------------------------------------------------------------------

Code/Mantid/Framework/DataHandling/CMakeLists.txt

@@ -136,6 +136,7 @@ set ( SRC_FILES
 	src/SaveParameterFile.cpp
 	src/SaveRKH.cpp
 	src/SaveReflTBL.cpp
+	src/SaveReflThreeColumnAscii.cpp
 	src/SaveSPE.cpp
 	src/SaveToSNSHistogramNexus.cpp
 	src/SaveVTK.cpp
@@ -277,6 +278,7 @@ set ( INC_FILES
 	inc/MantidDataHandling/SaveParameterFile.h
 	inc/MantidDataHandling/SaveRKH.h
 	inc/MantidDataHandling/SaveReflTBL.h
+	inc/MantidDataHandling/SaveReflThreeColumnAscii.h
 	inc/MantidDataHandling/SaveSPE.h
 	inc/MantidDataHandling/SaveToSNSHistogramNexus.h
 	inc/MantidDataHandling/SaveVTK.h
@@ -411,6 +413,7 @@ set ( TEST_FILES
 	SaveParameterFileTest.h
 	SaveRKHTest.h
 	SaveReflTBLTest.h
+	SaveReflThreeColumnAsciiTest.h
 	SaveSPETest.h
 	SaveToSNSHistogramNexusTest.h
 	SetSampleMaterialTest.h

Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/AsciiPointBase.h

@@ -60,8 +60,7 @@ namespace Mantid
       virtual void extraProps() = 0;
       /// write any extra information required
       virtual void extraHeaders(std::ofstream & file) = 0;
-      /// write the main content of the data
-      virtual void data(std::ofstream & file, const std::vector<double> & XData);
+
       /// Overwrites Algorithm method.
       void init();
       /// Overwrites Algorithm method
@@ -77,8 +76,11 @@ namespace Mantid
     protected:
       /// Return the separator character
       virtual char sep() {return '\t';}
+      /// write the main content of the data
+      virtual void data(std::ofstream & file, const std::vector<double> & XData, bool exportDeltaQ = true);
       double m_qres;
       size_t m_xlength;
+
       API::MatrixWorkspace_const_sptr m_ws;
     };
 

Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadNexusProcessed.h

@@ -6,6 +6,7 @@
 //----------------------------------------------------------------------
 #include "MantidAPI/IFileLoader.h"
 #include "MantidAPI/ITableWorkspace.h"
+#include "MantidAPI/MatrixWorkspace.h"
 
 #include "MantidNexus/NexusClasses.h"
 #include <nexus/NeXusFile.hpp>
@@ -15,6 +16,7 @@ namespace Mantid
 
   namespace DataHandling
   {
+
     /**
 
     Loads a workspace from a NeXus Processed entry in a NeXus file.
@@ -155,6 +157,9 @@ namespace Mantid
 
       /// calculates the workspace size
       std::size_t calculateWorkspacesize(const std::size_t numberofspectra);
+
+      /// Accellerated multiperiod loading
+      Mantid::API::Workspace_sptr doAccelleratedMultiPeriodLoading(Mantid::NeXus::NXRoot & root, const std::string & entryName, Mantid::API::MatrixWorkspace_sptr& tempMatrixWorkspace, const int64_t nWorkspaceEntries, const int64_t i);
 
       /// Does the current workspace have uniform binning
       bool m_shared_bins;

Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveReflCustomAscii.h

@@ -0,0 +1,71 @@
+#ifndef MANTID_DATAHANDLING_SaveReflCustomAscii_H_
+#define MANTID_DATAHANDLING_SaveReflCustomAscii_H_
+
+//----------------------------------------------------------------------
+// Includes
+//----------------------------------------------------------------------
+#include "MantidAPI/Algorithm.h"
+#include "MantidAPI/MatrixWorkspace.h"
+#include "MantidDataHandling/AsciiPointBase.h"
+
+namespace Mantid
+{
+  namespace DataHandling
+  {
+    /**
+    Saves a file in ILL Cosmos format  from a 2D workspace
+    (Workspace2D class). SaveILLCosmosAscii is an algorithm but inherits frrm the
+    AsciiPointBase class which provides the main implementation for the init() & exec() methods.
+    Output is tab delimited Ascii point data with dq/q and extra header information.
+
+    Copyright © 2007-14 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>
+    */
+    class DLLExport SaveReflCustomAscii : public DataHandling::AsciiPointBase
+    {
+    public:
+      /// Default constructor
+      SaveReflCustomAscii() {}
+      /// Destructor
+      ~SaveReflCustomAscii() {}
+      /// Algorithm's name for identification overriding a virtual method
+      virtual const std::string name() const { return "SaveReflCustomAscii"; }
+      ///Summary of algorithms purpose
+      virtual const std::string summary() const {return "Saves a 2D workspace to a ascii file.";}
+      /// Algorithm's version for identification overriding a virtual method
+      virtual int version() const { return 1; }
+
+
+      ///
+      void data(std::ofstream & file, const std::vector<double> & XData, bool exportDeltaQ);
+
+    private:
+
+      /// Return the file extension this algorthm should output.
+      virtual std::string ext() {return ".dat";}
+      ///extra properties specifically for this
+      virtual void extraProps();
+      /// write any extra information required
+      virtual void extraHeaders(std::ofstream & file);
+    };
+  } // namespace DataHandling
+} // namespace Mantid
+
+#endif  /*  MANTID_DATAHANDLING_SaveReflCustomAscii_H_  */

Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveReflThreeColumnAscii.h

@@ -0,0 +1,69 @@
+#ifndef MANTID_DATAHANDLING_SAVEREFLTHREECOLUMNASCII_H_
+#define MANTID_DATAHANDLING_SAVEREFLTHREECOLUMNASCII_H_
+
+//----------------------------------------------------------------------
+// Includes
+//----------------------------------------------------------------------
+#include "MantidAPI/Algorithm.h"
+#include "MantidAPI/MatrixWorkspace.h"
+#include "MantidDataHandling/AsciiPointBase.h"
+
+namespace Mantid
+{
+  namespace DataHandling
+  {
+    /**
+    Saves a file in three column format  from a 2D workspace
+    (Workspace2D class). SaveReflThreeColumnAscii is an algorithm but inherits from the
+    AsciiPointBase class which provides the main implementation for the init() & exec() methods.
+    Output is tab delimited Ascii point data without dq/q and with extra header information.
+
+    Copyright © 2007-14 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>
+    */
+    class DLLExport SaveReflThreeColumnAscii : public DataHandling::AsciiPointBase
+    {
+    public:
+      /// Default constructor
+      SaveReflThreeColumnAscii() {}
+      /// Destructor
+      ~SaveReflThreeColumnAscii() {}
+      /// Algorithm's name for identification overriding a virtual method
+      virtual const std::string name() const { return "SaveReflThreeColumnAscii"; }
+      ///Summary of algorithms purpose
+      virtual const std::string summary() const {return "Saves a 2D workspace to a ascii file.";}
+      /// Algorithm's version for identification overriding a virtual method
+      virtual int version() const { return 1; }
+      ///Algorithm's version for data output overriding a virtual method
+      void data(std::ofstream & file, const std::vector<double> & XData, bool exportDeltaQ = false);
+
+    private:
+
+      /// Return the file extension this algorthm should output.
+      virtual std::string ext() {return ".dat";}
+      ///extra properties specifically for this
+      virtual void extraProps();
+      /// write any extra information required
+      virtual void extraHeaders(std::ofstream & file);
+    };
+  } // namespace DataHandling
+} // namespace Mantid
+
+#endif  /*  MANTID_DATAHANDLING_SAVEREFLTHREECOLUMNASCII_H_  */

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

@@ -75,22 +75,38 @@ namespace Mantid
     /** virtual method to add information to the file before the data
      *  @param file :: pointer to output file stream
      *  @param XData :: pointer to a std::vector<double> containing the point data to be printed
+     *  @param exportDeltaQ :: bool on whether deltaQ column to be printed
      */
-    void AsciiPointBase::data(std::ofstream & file, const std::vector<double> & XData)
+    void AsciiPointBase::data(std::ofstream & file, const std::vector<double> & XData, bool exportDeltaQ)
     {
+
       const std::vector<double> & yData = m_ws->readY(0);
       const std::vector<double> & eData = m_ws->readE(0);
-      for (size_t i = 0; i < m_xlength; ++i)
+      if (exportDeltaQ)
       {
-        double dq = XData[i]*m_qres;
-        outputval(XData[i], file, leadingSep());
-        outputval(yData[i], file);
-        outputval(eData[i], file);
-        outputval(dq, file);
-        file << std::endl;
+        for (size_t i = 0; i < m_xlength; ++i)
+        {
+          double dq = XData[i]*m_qres;
+          outputval(XData[i], file, leadingSep());
+          outputval(yData[i], file);
+          outputval(eData[i], file);
+          outputval(dq, file);
+          file << std::endl;
+        }
+      }
+      else 
+      {
+        for (size_t i = 0; i < m_xlength; ++i)
+        {
+          outputval(XData[i], file, leadingSep());
+          outputval(yData[i], file);
+          outputval(eData[i], file);
+          file << std::endl;
+        }
       }
     }
 
+
     /** writes a properly formatted line of data
      *  @param val :: the double value to be written
      *  @param file :: pointer to output file stream