Merge pull request #646 from mantidproject/11362_SaveMD_MDHisto_struc…

…ture_change

Change SaveMD structure for MDHisto

Code/Mantid/Framework/MDAlgorithms/CMakeLists.txt

@@ -102,6 +102,7 @@ set ( SRC_FILES
 	src/ReflectometryTransformQxQz.cpp
 	src/SaveIsawQvector.cpp
 	src/SaveMD.cpp
+	src/SaveMD2.cpp
 	src/SaveZODS.cpp
 	src/SetMDUsingMask.cpp
 	src/SliceMD.cpp
@@ -220,6 +221,7 @@ set ( INC_FILES
 	inc/MantidMDAlgorithms/ReflectometryTransformQxQz.h
 	inc/MantidMDAlgorithms/SaveIsawQvector.h
 	inc/MantidMDAlgorithms/SaveMD.h
+	inc/MantidMDAlgorithms/SaveMD2.h
 	inc/MantidMDAlgorithms/SaveZODS.h
 	inc/MantidMDAlgorithms/SetMDUsingMask.h
 	inc/MantidMDAlgorithms/SliceMD.h
@@ -320,6 +322,7 @@ set ( TEST_FILES
 	ResolutionConvolvedCrossSectionTest.h
 	SaveIsawQvectorTest.h
 	SaveMDTest.h
+	SaveMD2Test.h
 	SaveZODSTest.h
 	SetMDUsingMaskTest.h
 	SimulateResolutionConvolvedModelTest.h

Code/Mantid/Framework/MDAlgorithms/inc/MantidMDAlgorithms/LoadMD.h

@@ -75,6 +75,8 @@ class DLLExport LoadMD : public API::IFileLoader<Kernel::NexusDescriptor> {
 
   void loadDimensions();
 
+  void loadDimensions2();
+
   void loadCoordinateSystem();
 
   /// Load all the affine matricies

Code/Mantid/Framework/MDAlgorithms/inc/MantidMDAlgorithms/SaveMD2.h

@@ -0,0 +1,70 @@
+#ifndef MANTID_MDALGORITHMS_SAVEMD2_H_
+#define MANTID_MDALGORITHMS_SAVEMD2_H_
+
+#include "MantidKernel/System.h"
+#include "MantidAPI/Algorithm.h"
+#include "MantidDataObjects/MDEventWorkspace.h"
+
+namespace Mantid {
+
+namespace MDAlgorithms {
+
+/** Save a MDEventWorkspace to a .nxs file.
+
+  Copyright © 2015 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 SaveMD2 : public API::Algorithm {
+public:
+  SaveMD2();
+  ~SaveMD2();
+
+  /// Algorithm's name for identification
+  virtual const std::string name() const { return "SaveMD"; };
+  /// Summary of algorithms purpose
+  virtual const std::string summary() const {
+    return "Save a MDEventWorkspace or MDHistoWorkspace to a .nxs file.";
+  }
+
+  /// Algorithm's version for identification
+  virtual int version() const { return 2; };
+  /// Algorithm's category for identification
+  virtual const std::string category() const { return "MDAlgorithms"; }
+
+private:
+  /// Initialise the properties
+  void init();
+  /// Run the algorithm
+  void exec();
+
+  /// Save the MDHistoWorkspace.
+  void doSaveHisto(Mantid::DataObjects::MDHistoWorkspace_sptr ws);
+
+  /// Save a generic matrix
+  template <typename T>
+  void saveMatrix(::NeXus::File *const file, std::string name,
+                  Kernel::Matrix<T> &m, ::NeXus::NXnumtype type,
+                  std::string tag = "");
+};
+
+} // namespace DataObjects
+} // namespace Mantid
+
+#endif /* MANTID_MDALGORITHMS_SAVEMD2_H_ */

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

@@ -158,17 +158,27 @@ void LoadMD::exec() {
   // Open the entry
   m_file->openGroup(entryName, "NXentry");
 
-  // How many dimensions?
-  std::vector<int32_t> vecDims;
-  m_file->readData("dimensions", vecDims);
-  if (vecDims.empty())
-    throw std::runtime_error("LoadMD:: Error loading number of dimensions.");
-  m_numDims = vecDims[0];
-  if (m_numDims <= 0)
-    throw std::runtime_error("LoadMD:: number of dimensions <= 0.");
-
-  // Now load all the dimension xml
-  this->loadDimensions();
+  // Check is SaveMD version 2 was used
+  int SaveMDVersion = 0;
+  if (m_file->hasAttr("SaveMDVersion"))
+    m_file->getAttr("SaveMDVersion", SaveMDVersion);
+
+  if (SaveMDVersion == 2)
+    this->loadDimensions2();
+  else {
+    // How many dimensions?
+    std::vector<int32_t> vecDims;
+    m_file->readData("dimensions", vecDims);
+    if (vecDims.empty())
+      throw std::runtime_error("LoadMD:: Error loading number of dimensions.");
+    m_numDims = vecDims[0];
+    if (m_numDims <= 0)
+      throw std::runtime_error("LoadMD:: number of dimensions <= 0.");
+
+    // Now load all the dimension xml
+    this->loadDimensions();
+  }
+
   // Coordinate system
   this->loadCoordinateSystem();
 
@@ -211,12 +221,19 @@ void LoadMD::loadSlab(std::string name, void *data, MDHistoWorkspace_sptr ws,
   if (m_file->getInfo().type != dataType)
     throw std::runtime_error("Unexpected data type for '" + name +
                              "' data set.'");
-  if (m_file->getInfo().dims[0] != static_cast<int>(ws->getNPoints()))
+
+  int nPoints = 1;
+  size_t numDims = m_file->getInfo().dims.size();
+  std::vector<int> size(numDims);
+  for (size_t d = 0; d < numDims; d++) {
+    nPoints *= static_cast<int>(m_file->getInfo().dims[d]);
+    size[d] = static_cast<int>(m_file->getInfo().dims[d]);
+  }
+  if (nPoints != static_cast<int>(ws->getNPoints()))
     throw std::runtime_error(
         "Inconsistency between the number of points in '" + name +
         "' and the number of bins defined by the dimensions.");
-  std::vector<int> start(1, 0);
-  std::vector<int> size(1, static_cast<int>(ws->getNPoints()));
+  std::vector<int> start(numDims, 0);
   try {
     m_file->getSlab(data, start, size);
   } catch (...) {
@@ -273,6 +290,37 @@ void LoadMD::loadDimensions() {
   }
 }
 
+//----------------------------------------------------------------------------------------------
+/** Load all the dimensions into this->m_dims
+* The dimensions are stored as an nxData array */
+void LoadMD::loadDimensions2() {
+  m_dims.clear();
+
+  std::string axes;
+
+  m_file->openData("signal");
+  m_file->getAttr("axes", axes);
+  m_file->closeData();
+
+  std::vector<std::string> splitAxes;
+  boost::split(splitAxes, axes, boost::is_any_of(":"));
+  // Create each dimension from axes data
+  // We loop axes backwards because Mantid
+  for (size_t d = splitAxes.size(); d > 0; d--) {
+    std::string long_name;
+    std::string units;
+    std::vector<double> axis;
+    m_file->openData(splitAxes[d - 1]);
+    m_file->getAttr("long_name", long_name);
+    m_file->getAttr("units", units);
+    m_file->getData(axis);
+    m_file->closeData();
+    m_dims.push_back(boost::make_shared<MDHistoDimension>(
+        long_name, splitAxes[d - 1], units, static_cast<coord_t>(axis.front()),
+        static_cast<coord_t>(axis.back()), axis.size() - 1));
+  }
+}
+
 /** Load the coordinate system **/
 void LoadMD::loadCoordinateSystem() {
   // Current version stores the coordinate system