Introduction of SaveCanSAS1D2.

This algorithm implements the CanSAS version 1.1

re #6839

Code/Mantid/Framework/DataHandling/CMakeLists.txt

@@ -112,6 +112,7 @@ set ( SRC_FILES
 	src/SaveCSV.cpp
 	src/SaveCalFile.cpp
 	src/SaveCanSAS1D.cpp
+	src/SaveCanSAS1D2.cpp
 	src/SaveDASC.cpp
 	src/SaveDaveGrp.cpp
 	src/SaveDetectorMasks.cpp
@@ -248,6 +249,7 @@ set ( INC_FILES
 	inc/MantidDataHandling/SaveCSV.h
 	inc/MantidDataHandling/SaveCalFile.h
 	inc/MantidDataHandling/SaveCanSAS1D.h
+	inc/MantidDataHandling/SaveCanSAS1D2.h
 	inc/MantidDataHandling/SaveDASC.h
 	inc/MantidDataHandling/SaveDaveGrp.h
 	inc/MantidDataHandling/SaveDetectorMasks.h

Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveCanSAS1D2.h

@@ -0,0 +1,101 @@
+#ifndef MANTID_DATAHANDLING_SAVECANSAS1D2_H
+#define MANTID_DATAHANDLING_SAVECANSAS1D2_H
+
+//----------------------------------------------------------------------
+// Includes
+//----------------------------------------------------------------------
+#include "MantidAPI/Algorithm.h"
+#include "SaveCanSAS1D.h"
+#include <fstream>  
+
+namespace Poco{
+  namespace XML{
+    class Document;
+    class Element;
+    class Text;
+  }
+}
+
+namespace Mantid
+{
+  namespace DataHandling
+  {
+    /** @class SaveCanSAS1D2  DataHandling/SaveCanSAS1D2.h
+
+    @verbatim
+
+    This algorithm saves  workspace into CanSAS1d format. This is an xml format except
+    the <Idata>, </Idata> tags and all data in between must be one line, which necesitates
+    the files be written iostream functions outside xml libraries.
+
+    The second version of CanSAS1D implements the version 1.1, whose schema is found at
+    http://www.cansas.org/formats/1.1/cansas1d.xsd. See the tutorial for more infomation 
+    about: http://www.cansas.org/svn/1dwg/trunk/doc/cansas-1d-1_1-manual.pdf.
+ 
+    The first version of SaveCanSAS1D implemented the version 1.0 of CanSAS.
+    The main difference among them is the definition of the SASRoot and the 
+    introduction of a new element called SAStransmission_spectrum, which allows
+    to record the Spectrum of the transmission for the sample and can. 
+
+    So, the SaveCanSAS1D2 will extend SaveCanSAS1D in the following: 
+    
+     - Introduction of 2 new (optional) workspace properties:
+       - Transmission - The workspace for of the transmission
+       - TransmissionCan - The workspace for the transmission can
+     - Extension of the ::init method in order to introduce these workspaces properties.
+     - Overide the ::createSASRootElement to conform the new header. 
+     - Introduction of the method to deal with the new element: ::createSASTransElement. 
+     - Override the ::exec method to introduce this new element when apropriated. 
+       
+    @author Gesner Passos, Rutherford Appleton Laboratory
+    @date 11/04/2013
+
+    Copyright &copy; 2007-10 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 SaveCanSAS1D2 : public SaveCanSAS1D
+    {
+    public:
+      /// default constructor
+      SaveCanSAS1D2();
+      virtual ~SaveCanSAS1D2();
+
+      /// Algorithm's version for identification overriding a virtual method
+      virtual int version() const { return 2; }
+    protected:
+      /// Extends the SaveCanSAS1D init method
+      virtual void init();
+      /// Overwrites Algorithm method
+      virtual void exec();
+
+      /// Create the SASRoot element
+      virtual void createSASRootElement(std::string& rootElem);
+
+      /// this method creates SAStransmission_spectrum element
+      void createSASTransElement(std::string& sasTrans, const std::string & name  );
+
+      ///points to the workspace that will be written to file
+      API::MatrixWorkspace_const_sptr m_trans_ws, m_transcan_ws;
+    };
+
+  }
+}
+
+#endif

Code/Mantid/Framework/DataHandling/src/SaveCanSAS1D2.cpp

@@ -0,0 +1,269 @@
+/*WIKI* 
+
+Saves the given workspace to a file which will be in canSAS 1-D format specified by canSAS 1-D Data Formats Working Group schema http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd. CANSAS has a Wiki page at  http://www.smallangles.net/wgwiki/index.php/canSAS_Working_Groups.
+
+The second version is compatible with canSAS - 1D - Version 1.1. If you need to save to the version 1.0 please
+use the first version of this algorithm. You can see it at: [SaveCanSAS1D_1.0].
+
+Workspace group members and appended workspaces are stored in separate SASentry [http://en.wikipedia.org/wiki/Xml xml] elements.
+
+This algorithm saves  workspace into CanSAS1d format. This is an xml format except
+the <Idata>, </Idata> tags and all data in between must be one line, which necesitates
+the files be written iostream functions outside xml libraries.
+
+The second version of CanSAS1D implements the version 1.1, whose schema is found at
+http://www.cansas.org/formats/1.1/cansas1d.xsd. See the tutorial for more infomation 
+about: http://www.cansas.org/svn/1dwg/trunk/doc/cansas-1d-1_1-manual.pdf.
+
+The structure of CanSAS1d xml is defined at the links above.
+
+*WIKI*/
+//----------------------------------------------------------------------
+// Includes
+//----------------------------------------------------------------------
+#include "MantidDataHandling/SaveCanSAS1D2.h"
+#include "MantidAPI/FileProperty.h"
+#include "MantidKernel/Exception.h"
+#include "MantidGeometry/IComponent.h"
+#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidKernel/MantidVersion.h"
+#include "MantidKernel/ListValidator.h"
+#include "MantidAPI/Run.h"
+#include <boost/shared_ptr.hpp>
+
+//-----------------------------------------------------------------------------
+using namespace Mantid::Kernel;
+using namespace Mantid::Geometry;
+using namespace Mantid::API;
+
+namespace Mantid
+{
+namespace DataHandling
+{
+
+// Register the algorithm into the AlgorithmFactory
+DECLARE_ALGORITHM(SaveCanSAS1D2)
+
+    /// constructor
+    SaveCanSAS1D2::SaveCanSAS1D2()
+{}
+
+/// destructor
+SaveCanSAS1D2::~SaveCanSAS1D2()
+{}
+
+/// Overwrites Algorithm method.
+void SaveCanSAS1D2::init()
+{
+  SaveCanSAS1D::init(); 
+
+  declareProperty(new API::WorkspaceProperty<>("Transmission","",Kernel::Direction::Input,PropertyMode::Optional,
+                                               boost::make_shared<API::WorkspaceUnitValidator>("Wavelength")),"The transmission workspace. Optional. If given, will be saved at TransmissionSpectrum"); 
+
+  declareProperty(new API::WorkspaceProperty<>("TransmissionCan","",Kernel::Direction::Input,PropertyMode::Optional,
+                                               boost::make_shared<API::WorkspaceUnitValidator>("Wavelength")),"The transmission workspace of the Can. Optional. If given, will be saved at TransmissionSpectrum"); 
+
+}
+
+/// Overwrites Algorithm method
+void SaveCanSAS1D2::exec()
+{
+  m_workspace = getProperty("InputWorkspace");
+  m_trans_ws = getProperty("Transmission"); 
+  m_transcan_ws = getProperty("TransmissionCan"); 
+  if( ! m_workspace )
+  {
+    throw std::invalid_argument("Invalid inputworkspace ,Error in  SaveCanSAS1D");
+  }
+
+  if (m_workspace->getNumberHistograms() > 1)
+  {
+    throw std::invalid_argument("Error in SaveCanSAS1D - more than one histogram.");
+  }
+
+  if ((m_trans_ws && m_trans_ws->getNumberHistograms() > 1)
+      ||
+      (m_transcan_ws && m_transcan_ws->getNumberHistograms() > 1)){
+    throw std::invalid_argument("Error in SaveCanSAS1D - more than one histogram for the transmission workspaces"); 
+  }
+
+  // write xml manually as the user requires a specific format were the placement of new line characters is controled
+  //and this can't be done in using the stylesheet part in Poco or libXML 
+  prepareFileToWriteEntry();
+
+  m_outFile << "\n\t<SASentry name=\"" << m_workspace->getName() << "\">";
+
+  std::string sasTitle;
+  createSASTitleElement(sasTitle);
+  m_outFile<<sasTitle;
+
+  std::string sasRun;
+  createSASRunElement(sasRun);
+  m_outFile<<sasRun;
+
+  std::string dataUnit = m_workspace->YUnitLabel();
+  //look for xml special characters and replace with entity refrence
+  searchandreplaceSpecialChars(dataUnit);
+
+
+  std::string sasData;
+  createSASDataElement(sasData);
+  m_outFile<<sasData;
+
+  if (m_trans_ws){
+    std::string transData; 
+    createSASTransElement(transData, "sample"); 
+    m_outFile << transData;
+  }
+  if (m_transcan_ws){
+    std::string transData; 
+    createSASTransElement(transData, "can"); 
+    m_outFile << transData; 
+  }
+
+  std::string sasSample;
+  createSASSampleElement(sasSample);
+  m_outFile<<sasSample;
+
+  std::string sasInstr="\n\t\t<SASinstrument>";
+  m_outFile<<sasInstr;
+  std::string sasInstrName="\n\t\t\t<name>";
+  std::string instrname=m_workspace->getInstrument()->getName();
+  //look for xml special characters and replace with entity refrence
+  searchandreplaceSpecialChars(instrname);
+  sasInstrName+=instrname;
+  sasInstrName+="</name>";
+  m_outFile<<sasInstrName;
+
+  std::string sasSource;
+  createSASSourceElement(sasSource);
+  m_outFile<<sasSource;
+
+  std::string sasCollimation="\n\t\t\t<SAScollimation/>";
+  m_outFile<<sasCollimation;
+
+
+  try
+  {
+    std::string sasDet;
+    createSASDetectorElement(sasDet);
+    m_outFile<<sasDet;
+  }
+  catch(Kernel::Exception::NotFoundError&)
+  {
+    m_outFile.close();
+    throw;
+  }
+  catch(std::runtime_error& )
+  {
+    m_outFile.close();
+    throw ;
+  }
+
+  sasInstr="\n\t\t</SASinstrument>";
+  m_outFile<<sasInstr;
+
+  std::string sasProcess;
+  createSASProcessElement(sasProcess);
+  m_outFile<<sasProcess;
+
+  // Reduction process, if available
+  const std::string process_xml = getProperty("Process");
+  if (process_xml.size()>0)
+  {
+    m_outFile << "\n\t\t<SASProcess>\n";
+    m_outFile << process_xml;
+    m_outFile << "\n\t\t</SASProcess>\n";
+  }
+
+  std::string sasNote="\n\t\t<SASnote>";
+  sasNote+="\n\t\t</SASnote>";
+  m_outFile<<sasNote;
+
+  m_outFile << "\n\t</SASentry>";
+  m_outFile << "\n</SASroot>";
+  m_outFile.close();
+}
+
+
+/** This method creates an XML element named "SASroot"
+ *  @param rootElem ::  xml root element string
+ */
+void SaveCanSAS1D2::createSASRootElement(std::string& rootElem)
+{
+  rootElem="<SASroot version=\"1.1\"";
+  rootElem +="\n\t\t xmlns=\"urn:cansas1d:1.1\"";
+  rootElem+="\n\t\t xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"";
+  rootElem+="\n\t\t xsi:schemaLocation=\"urn:cansas1d:1.1 http://www.cansas.org/formats/1.1/cansas1d.xsd\"\n\t\t>";
+}
+
+/** This method creates an XML element named "SAStransmission_spectrum"
+ *  @param sasData :: string for sasdata element in the xml
+ * @param name :: name of the type of spectrum. Two values are acceptable: sample, can
+ */
+void SaveCanSAS1D2::createSASTransElement(std::string& sasTrans, const std::string & name)
+{
+  API::MatrixWorkspace_const_sptr m_ws;
+  if (name == "sample"){
+    m_ws = m_trans_ws;
+  }else if (name == "can"){
+    m_ws = m_transcan_ws; 
+  }else{
+    return ; // does not change sasTrans... it will add nothing
+  }
+
+  if (m_ws->getNumberHistograms() != 1)
+    return; // does not change sasTrans
+
+  std::stringstream trans;
+
+  trans << "\n\t\t<SAStransmission_spectrum name=\""
+        << name 
+        << "\">";
+  std::string t_unit = m_ws->YUnitLabel(); 
+  std::string lambda_unit;// = m_ws->getUnits(); FIXME: how to get the unit
+  if (t_unit.empty())
+    t_unit = "none"; 
+  if (lambda_unit.empty())
+    lambda_unit = "A";
+
+  const MantidVec& xdata = m_ws->readX(0);
+  const MantidVec& ydata = m_ws->readY(0);
+  const MantidVec& edata = m_ws->readE(0);
+  const bool isHistogram = m_ws->isHistogramData();
+  double lambda, trans_value, trans_err; 
+  for (size_t j = 0; j < m_workspace->blocksize(); ++j)
+  {
+    // x data is the Lambda in xml. If histogramdata take the mean
+    lambda = isHistogram ? (xdata[j] + xdata[j+1])/2: xdata[j];
+    // y data is the T in xml.
+    trans_value = ydata[j]; 
+    // e data is the Tdev in xml. 
+    trans_err = edata[j]; 
+
+    trans << "\n\t\t\t<Tdata><Lambda unit=\""<<lambda_unit
+          <<"\">"; 
+    if (lambda == lambda) // check for NAN
+      trans << lambda ; 
+    else 
+      trans << "NaN";
+    trans << "</Lambda>"
+          <<"<T unit=\""<< t_unit <<"\">";
+    if (trans_value == trans_value)
+      trans << trans_value; 
+    else
+      trans << "NaN"; 
+    trans << "</T><Tdev unit=\"none\">";
+    if (trans_err == trans_err)
+      trans << trans_err; 
+    else
+      trans << "NaN"; 
+    trans  << "</Tdev></Tdata>";
+  }
+  trans << "\n\t\t</SAStransmission_spectrum>";
+  sasTrans += trans.str(); 
+}
+
+}
+
+}